GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcvP in Dinoroseobacter shibae DFL-12

Align Glycine dehydrogenase (aminomethyl-transferring) (EC 1.4.4.2) (characterized)
to candidate 3609294 Dshi_2680 glycine dehydrogenase (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1868
         (950 letters)



>FitnessBrowser__Dino:3609294
          Length = 954

 Score = 1153 bits (2983), Expect = 0.0
 Identities = 570/940 (60%), Positives = 697/940 (74%), Gaps = 10/940 (1%)

Query: 15  RHIGPRAGDEQAMLNSLGFDSLEALSASVIPDSIKGTSVLGLEDGLSEADALALIKSIAT 74
           RHIGP   +   ML +LG  SLEAL    +P+ I+    L     LSE D L  ++ +A 
Sbjct: 17  RHIGPSPKEMGQMLATLGVPSLEALINEALPEGIRRRDPLAFGPALSERDTLHRMRELAD 76

Query: 75  KNQLFKTFIGQGYYGTHTPSPILRNLLENPAWYTAYTPYQPEISQGRLEALLNFQTLISD 134
           KN +  + IGQGY+GTHTP  ILRN+LENPAWYTAYTPYQPEISQGRLEALLNFQT+++D
Sbjct: 77  KNTVLTSLIGQGYHGTHTPPVILRNILENPAWYTAYTPYQPEISQGRLEALLNFQTMMAD 136

Query: 135 LTGLPIANASLLDEATAAAEAMTFCKRLSKNKGSHAFFASVHCHPQTLDVLRTRAEPLGI 194
           LTGLPIANASLLDE TAAAEAM   +R SK+K +  FF +  CHPQT+DV+RTRAEPLGI
Sbjct: 137 LTGLPIANASLLDEGTAAAEAMAMAQRASKSK-ARGFFVAEDCHPQTIDVIRTRAEPLGI 195

Query: 195 DVVVGDERELTDVTPFFGALLQYPASNGDVFDYRELTERFHAANALVAVAADLLALTVLT 254
           +V+VG    L D    F AL QYP S G V DY ++ E  H A AL  VAAD LALT+L 
Sbjct: 196 EVIVGAVDAL-DPEAVFAALFQYPGSYGHVRDYSDVIEALHGARALAVVAADPLALTLLK 254

Query: 255 APGEFGADVAIGSAQRFGVPLGFGGPHAAYFSTKDAFKRDMPGRLVGVSVDRFGNPALRL 314
           +PGE GAD+AIGS QRFGVP+G+GGPHAAY +  DA KR MPGR++GVSVD  GN A RL
Sbjct: 255 SPGEMGADIAIGSTQRFGVPMGYGGPHAAYMTCTDALKRSMPGRIIGVSVDARGNKAYRL 314

Query: 315 AMQTREQHIRREKATSNICTAQVLLANIASMYAVYHGPKGLTQIANRVHHLTAILAKGLS 374
           ++QTREQHIRREKA SN+CTAQ LLA +ASMY V+HGP GL  IA  VH  TA +A GL+
Sbjct: 315 SLQTREQHIRREKANSNVCTAQALLAVMASMYGVFHGPDGLKAIAQTVHRKTARMADGLT 374

Query: 375 ALGLSVEQASFFDTLTVKAGAQTAALHDKAHAQRINLRVVDGERLGLSLDETTTQADVET 434
            LG  V+   +FDT+TVK G+    +   A  + +NLR V  +R+G++LDE T    +E 
Sbjct: 375 ELGFKVDPQDYFDTITVKVGSMQGVILAAALREGVNLRKVGTDRIGITLDELTLGRTIEA 434

Query: 435 LWSLLSDGKALPDFAALAASVQSAIPATLVRQSPILSHPVFNRYHSETELMRYLRKLADK 494
           +W        + D   +       +P  ++R+S  ++HP+F+   +E E+ RY+R+LAD+
Sbjct: 435 VWRAFGAEGMVYDKTRMVYH----LPQEMLRESSYMTHPIFHMNRAEAEMTRYMRRLADR 490

Query: 495 DLALDRTMIPLGSCTMKLNAASEMIPVTWAEFGALHPFAPAEQSAGYQQLTDELEAMLCA 554
           DLALDR MIPLGSCTMKLNA  EM+P+TW EF  LHPFAPA+Q+AGY ++  EL  MLC 
Sbjct: 491 DLALDRAMIPLGSCTMKLNATVEMLPLTWPEFANLHPFAPADQAAGYHEMIAELSQMLCD 550

Query: 555 ATGYDSVSLQPNAGSQGEYAGLLAIRAYHQSRGEDRRDICLIPSSAHGTNPATAQMAGMR 614
            TGYD++S+QPN+G+QGEYAGLLAIR YH++RGE  R+ICLIP+SAHGTNPA+AQM G +
Sbjct: 551 VTGYDAMSMQPNSGAQGEYAGLLAIRGYHRARGEGHRNICLIPTSAHGTNPASAQMVGWK 610

Query: 615 VVVTACDARGNVDIEDLRAKAIEHREHLAALMITYPSTHGVFEEGIREICGIIHDNGGQV 674
           VVV      G++D+ED RAKA +H E+LA  MITYPSTHGVFEE +RE+C I H +GGQV
Sbjct: 611 VVVVKSAENGDIDLEDFRAKAEQHSENLAGCMITYPSTHGVFEEIVREVCDITHAHGGQV 670

Query: 675 YIDGANMNAMVGLCAPGKFGGDVSHLNLHKTFCIPHGGGGPGVGPIGVKSHLAPFLPGHA 734
           YIDGANMNAMVGL APG  GGDVSHLNLHKTFCIPHGGGGPG+GPIGVK+HLAP LP HA
Sbjct: 671 YIDGANMNAMVGLSAPGDLGGDVSHLNLHKTFCIPHGGGGPGMGPIGVKAHLAPHLPSHA 730

Query: 735 QME----RKEGAVCAAPFGSASILPITWMYIRMMGGAGLKRASQLAILNANYISRRLEEH 790
                     GAV +A +GS SIL I++ Y  +MGGAGL +A+++AILNANY+++RL   
Sbjct: 731 TATGAGFGDAGAVASAAYGSPSILTISYAYCLLMGGAGLTQATKVAILNANYMAKRLSAG 790

Query: 791 YPVLYTGSNGLVAHECILDLRPLKDSSGISVDDVAKRLIDFGFHAPTMSFPVAGTLMIEP 850
           +P+LY    G VAHECILD R L   +G++V+DVAKRL+D GFHAPTMS+PVAGTLM+EP
Sbjct: 791 FPILYANDKGRVAHECILDTRVLDKIAGVTVEDVAKRLMDCGFHAPTMSWPVAGTLMVEP 850

Query: 851 TESESKEELDRFCDAMIRIREEIRAVENGTLDKDDNPLKNAPHTAKELVGEWSHPYSREQ 910
           TESE K ELDRFCDAM+ IREE  A+  G+LD ++NPLK APHT ++LVG+W  PYSREQ
Sbjct: 851 TESEPKAELDRFCDAMLAIREEADAIAAGSLDAENNPLKRAPHTVEDLVGDWDRPYSREQ 910

Query: 911 AVYPVASLIEGKYWPPVGRVDNVFGDRNLVCACPSIESYA 950
           A YP  +    KYWPPV RVDN +GDRNLVC CP +E YA
Sbjct: 911 ACYPPGAFRVDKYWPPVNRVDNAYGDRNLVCTCPPVEDYA 950


Lambda     K      H
   0.319    0.135    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 2257
Number of extensions: 91
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 950
Length of database: 954
Length adjustment: 44
Effective length of query: 906
Effective length of database: 910
Effective search space:   824460
Effective search space used:   824460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)

Align candidate 3609294 Dshi_2680 (glycine dehydrogenase (RefSeq))
to HMM TIGR00461 (gcvP: glycine dehydrogenase (EC 1.4.4.2))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00461.hmm
# target sequence database:        /tmp/gapView.7427.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00461  [M=939]
Accession:   TIGR00461
Description: gcvP: glycine dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
          0 1418.8   0.0          0 1418.6   0.0    1.0  1  lcl|FitnessBrowser__Dino:3609294  Dshi_2680 glycine dehydrogenase 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3609294  Dshi_2680 glycine dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1418.6   0.0         0         0       1     939 []      17     943 ..      17     943 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1418.6 bits;  conditional E-value: 0
                         TIGR00461   1 rhlGpdeaeqkkmlktlGfddlnalieqlvpkdirlarplkleapakeyealaelkkiasknkkvksyiGkGyyati 77 
                                       rh+Gp++ e+ +ml tlG+ +l+ali++++p+ ir + pl ++ + +e ++l +++++a+kn +++s iG+Gy +t 
  lcl|FitnessBrowser__Dino:3609294  17 RHIGPSPKEMGQMLATLGVPSLEALINEALPEGIRRRDPLAFGPALSERDTLHRMRELADKNTVLTSLIGQGYHGTH 93 
                                       9**************************************************************************** PP

                         TIGR00461  78 lppviqrnllenpgwytaytpyqpeisqGrleallnfqtvvldltGlevanaslldegtaaaeamalsfrvskkkan 154
                                       +ppvi+rn+lenp wytaytpyqpeisqGrleallnfqt++ dltGl++anaslldegtaaaeama+++r sk+ka 
  lcl|FitnessBrowser__Dino:3609294  94 TPPVILRNILENPAWYTAYTPYQPEISQGRLEALLNFQTMMADLTGLPIANASLLDEGTAAAEAMAMAQRASKSKAR 170
                                       ***************************************************************************** PP

                         TIGR00461 155 kfvvakdvhpqtlevvktraeplgievivddaskvkkavdvlGvllqypatdGeildykalidelksrkalvsvaad 231
                                        f+va+d+hpqt++v++traeplgieviv+ ++   +   v+ +l qyp++ G++ dy ++i++l+  +al  vaad
  lcl|FitnessBrowser__Dino:3609294 171 GFFVAEDCHPQTIDVIRTRAEPLGIEVIVGAVD-ALDPEAVFAALFQYPGSYGHVRDYSDVIEALHGARALAVVAAD 246
                                       ****************************99765.567889************************************* PP

                         TIGR00461 232 llaltlltppgklGadivlGsaqrfGvplGyGGphaaffavkdeykrklpGrivGvskdalGntalrlalqtreqhi 308
                                       +laltll++pg++Gadi++Gs+qrfGvp+GyGGphaa++++ d +kr++pGri+Gvs da Gn a rl+lqtreqhi
  lcl|FitnessBrowser__Dino:3609294 247 PLALTLLKSPGEMGADIAIGSTQRFGVPMGYGGPHAAYMTCTDALKRSMPGRIIGVSVDARGNKAYRLSLQTREQHI 323
                                       ***************************************************************************** PP

                         TIGR00461 309 rrdkatsnictaqvllanvaslyavyhGpkGlkniarrifrltsilaaglkrknyelrnktyfdtltvevgekaase 385
                                       rr+ka+sn+ctaq+lla++as+y+v+hGp Glk ia+ ++r t+ +a gl + ++++  + yfdt+tv+vg   +  
  lcl|FitnessBrowser__Dino:3609294 324 RREKANSNVCTAQALLAVMASMYGVFHGPDGLKAIAQTVHRKTARMADGLTELGFKVDPQDYFDTITVKVGSMQG-V 399
                                       ***********************************************************************9999.7 PP

                         TIGR00461 386 vlkaaeeaeinlravvltevgialdetttkedvldllkvlagkdnlglsseelsedvansfpaellrddeilrdevf 462
                                       +l aa   ++nlr v ++ +gi+lde t  + ++ +++ + ++  + +++      +   +p+e+lr++ ++++++f
  lcl|FitnessBrowser__Dino:3609294 400 ILAAALREGVNLRKVGTDRIGITLDELTLGRTIEAVWRAFGAEG-MVYDKT----RMVYHLPQEMLRESSYMTHPIF 471
                                       88899999********************************9954.444433....344579**************** PP

                         TIGR00461 463 nryhsetellrylhrleskdlalnqsmiplGsctmklnataemlpitwpefaeihpfapaeqveGykeliaqlekwl 539
                                       ++  +e+e+ ry+ rl  +dlal+++miplGsctmklnat+emlp+twpefa++hpfapa+q+ Gy+e+ia+l + l
  lcl|FitnessBrowser__Dino:3609294 472 HMNRAEAEMTRYMRRLADRDLALDRAMIPLGSCTMKLNATVEMLPLTWPEFANLHPFAPADQAAGYHEMIAELSQML 548
                                       ***************************************************************************** PP

                         TIGR00461 540 veitGfdaislqpnsGaqGeyaGlrvirsyhesrgeehrniclipasahGtnpasaamaGlkvvpvkcdkeGnidlv 616
                                       +++tG+da+s+qpnsGaqGeyaGl +ir yh +rge+hrniclip+sahGtnpasa+m+G kvv+vk  ++G+idl+
  lcl|FitnessBrowser__Dino:3609294 549 CDVTGYDAMSMQPNSGAQGEYAGLLAIRGYHRARGEGHRNICLIPTSAHGTNPASAQMVGWKVVVVKSAENGDIDLE 625
                                       ***************************************************************************** PP

                         TIGR00461 617 dlkakaekagdelaavmvtypstyGvfeetirevidivhrfGGqvyldGanmnaqvGltspgdlGadvchlnlhktf 693
                                       d++akae+++++la  m+typst+Gvfee +rev+di h  GGqvy+dGanmna vGl++pgdlG dv+hlnlhktf
  lcl|FitnessBrowser__Dino:3609294 626 DFRAKAEQHSENLAGCMITYPSTHGVFEEIVREVCDITHAHGGQVYIDGANMNAMVGLSAPGDLGGDVSHLNLHKTF 702
                                       ***************************************************************************** PP

                         TIGR00461 694 siphGGGGpgmgpigvkshlapflpktdlvsvvelegesksigavsaapyGsasilpisymyikmmGaeGlkkasev 770
                                       +iphGGGGpgmgpigvk+hlap+lp    + ++++ g     gav++a yGs sil+isy+y  +mG  Gl++a++v
  lcl|FitnessBrowser__Dino:3609294 703 CIPHGGGGPGMGPIGVKAHLAPHLPS---HATATGAGF-GDAGAVASAAYGSPSILTISYAYCLLMGGAGLTQATKV 775
                                       **************************...667776655.5689********************************** PP

                         TIGR00461 771 ailnanylakrlkdaykilfvgrdervahecildlrelkekagiealdvakrlldyGfhaptlsfpvaGtlmvepte 847
                                       ailnany+akrl   ++il+ + ++rvahecild r l + ag+ ++dvakrl+d Gfhapt+s+pvaGtlmvepte
  lcl|FitnessBrowser__Dino:3609294 776 AILNANYMAKRLSAGFPILYANDKGRVAHECILDTRVLDKIAGVTVEDVAKRLMDCGFHAPTMSWPVAGTLMVEPTE 852
                                       ***************************************************************************** PP

                         TIGR00461 848 sesleeldrfidamiaikeeidavkaGeiklednilknaphslqslivaewadpysreeaaypapvlkyfkfwptva 924
                                       se + eldrf+dam+ai+ee+da+ aG +++e+n+lk aph++++l v++w  pysre+a+yp +  +  k+wp v+
  lcl|FitnessBrowser__Dino:3609294 853 SEPKAELDRFCDAMLAIREEADAIAAGSLDAENNPLKRAPHTVEDL-VGDWDRPYSREQACYPPGAFRVDKYWPPVN 928
                                       *****************************************99985.79**************************** PP

                         TIGR00461 925 rlddtyGdrnlvcsc 939
                                       r+d++yGdrnlvc+c
  lcl|FitnessBrowser__Dino:3609294 929 RVDNAYGDRNLVCTC 943
                                       **************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (939 nodes)
Target sequences:                          1  (954 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.04u 0.03s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 13.44
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory