GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Phaeobacter inhibens BS107

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate GFF2791 PGA1_c28340 isocitrate dehydrogenase [NADP]

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__Phaeo:GFF2791
          Length = 790

 Score =  809 bits (2089), Expect = 0.0
 Identities = 422/738 (57%), Positives = 528/738 (71%), Gaps = 7/738 (0%)

Query: 2   STPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQK 61
           STP I+YT+ DEAP LA+ SLLPII++F  ++G++V T+DISLAGR++ATFPE L+D Q+
Sbjct: 57  STPDILYTIVDEAPELASASLLPIIRSFAAAAGVSVGTKDISLAGRILATFPEALSDAQR 116

Query: 62  ISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKD 121
            S+DLAELG+L  TP+AN+IKLPNISASVPQL AAI ELQ QG+ +PDYP +P TD EK+
Sbjct: 117 QSNDLAELGQLVKTPEANVIKLPNISASVPQLTAAIAELQAQGFGIPDYPADPATDAEKE 176

Query: 122 VKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDF 181
           ++ARYD IKGSAVNPVLREGNSDRRA  +VKN+A+ +PH MG WSADSK+ V+ M   DF
Sbjct: 177 IRARYDTIKGSAVNPVLREGNSDRRAAKAVKNFAQNNPHSMGKWSADSKTKVSSMLGNDF 236

Query: 182 YGSEKAALIGAP--GSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAE 239
           Y +E +A I A   G+ KIE + KDG+ TVLK    ++ G + D++ MS  AL +F+   
Sbjct: 237 YANEVSATISAAQAGTAKIEFVGKDGAVTVLKDSWPLEEGTVADATFMSAKALSSFLKDA 296

Query: 240 IEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGD 299
           IED K  G + S+H+KATMMKVSDPI+FG  V  +      K    ++  G   N+G+G 
Sbjct: 297 IEDTKADGTMFSLHMKATMMKVSDPIIFGHAVKAWLGPVWDKFGAEIEAAGGSANSGLGA 356

Query: 300 LYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 359
           + A I  LP      I+A+I A+   RP + MV+SDKGITNLHVPSDVI+DASMPA+IR 
Sbjct: 357 VLATIDGLPNGDA--IKAEIAAL--DRPSMYMVDSDKGITNLHVPSDVIIDASMPAVIRA 412

Query: 360 SGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEE 419
            GK W   G   DT  VIPDRCY+ VY   I   K +GA D TT GSV NVGLMAQKAEE
Sbjct: 413 GGKGWDEAGNKGDTNCVIPDRCYSTVYDESINFFKANGALDVTTAGSVANVGLMAQKAEE 472

Query: 420 YGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARA 479
           YGSH  TF+ PADG +R+   +G+ L    VEAGDIWR C  K API++W++LA++R R 
Sbjct: 473 YGSHPTTFEAPADGTIRIVLANGETLHAHEVEAGDIWRSCTVKKAPIENWIELAMDRQRL 532

Query: 480 TNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTI 539
           T + A+FWLD  RAHDA++I  V   L+    S L  +I++P EAT  SL  I  GKD+I
Sbjct: 533 TGSEAIFWLDENRAHDAELIKYVTPALEAAGKSDL-FQIMAPREATAQSLKTITAGKDSI 591

Query: 540 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYL 599
           ++TGNVLRDYLTDLFPI+ELGTSAKMLSIV LM+GGGLFETGAGGSAPKHVQQ +EE +L
Sbjct: 592 AITGNVLRDYLTDLFPILELGTSAKMLSIVKLMNGGGLFETGAGGSAPKHVQQLVEENHL 651

Query: 600 RWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGS 659
           RWDS+GEF AL  SL  L ++  N KA VL +  + AT  ILD+N+SP+RKVGE DNR S
Sbjct: 652 RWDSMGEFCALGESLNFLADSKGNAKAGVLGAAAEAATQGILDHNRSPSRKVGEPDNRAS 711

Query: 660 HFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPN 719
           H++ A YWA+ALAAQ +D EL A F  IA  L   E  I+ ELA  QGK VD+ GY+H +
Sbjct: 712 HYWFARYWAEALAAQGDDAELAAHFAPIAAELAAKEEAILSELAEVQGKAVDLGGYFHAD 771

Query: 720 TDLTSKAIRPSATFNAAL 737
              T+  +RPSAT N  +
Sbjct: 772 PVKTAAVMRPSATLNGII 789


Lambda     K      H
   0.315    0.131    0.374 

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: 1396
Number of extensions: 46
Number of successful extensions: 4
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: 741
Length of database: 790
Length adjustment: 40
Effective length of query: 701
Effective length of database: 750
Effective search space:   525750
Effective search space used:   525750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 55 (25.8 bits)

Align candidate GFF2791 PGA1_c28340 (isocitrate dehydrogenase [NADP])
to HMM TIGR00178 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

# 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/TIGR00178.hmm
# target sequence database:        /tmp/gapView.6242.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00178  [M=744]
Accession:   TIGR00178
Description: monomer_idh: isocitrate dehydrogenase, NADP-dependent
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 1071.8   1.5          0 1071.6   1.5    1.0  1  lcl|FitnessBrowser__Phaeo:GFF2791  PGA1_c28340 isocitrate dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF2791  PGA1_c28340 isocitrate dehydrogenase [NADP]
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1071.6   1.5         0         0       5     739 ..      58     789 ..      53     790 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1071.6 bits;  conditional E-value: 0
                          TIGR00178   5 kakiiytltdeapllatysllpivkafaasaGievetrdislagrilaefpeylteeqkvddalaelGelaktpea 80 
                                        ++ i+yt+ deap la+ sllpi+++faa+aG++v t+dislagrila+fpe l++ q+ +++laelG+l ktpea
  lcl|FitnessBrowser__Phaeo:GFF2791  58 TPDILYTIVDEAPELASASLLPIIRSFAAAAGVSVGTKDISLAGRILATFPEALSDAQRQSNDLAELGQLVKTPEA 133
                                        578************************************************************************* PP

                          TIGR00178  81 niiklpnisasvpqlkaaikelqdkGydlpdypeepktdeekdikaryakikGsavnpvlreGnsdrraplavkey 156
                                        n+iklpnisasvpql+aai elq++G+ +pdyp++p td+ek+i+ary+ ikGsavnpvlreGnsdrra +avk++
  lcl|FitnessBrowser__Phaeo:GFF2791 134 NVIKLPNISASVPQLTAAIAELQAQGFGIPDYPADPATDAEKEIRARYDTIKGSAVNPVLREGNSDRRAAKAVKNF 209
                                        **************************************************************************** PP

                          TIGR00178 157 arkhphkmGewsadskshvahmdagdfyaseksvlldaae..evkieliakdGketvlkaklklldgevidssvls 230
                                        a+++ph+mG+wsadsk++v+ m  +dfya+e s+++ aa+    kie++ kdG +tvlk++ +l++g v d++++s
  lcl|FitnessBrowser__Phaeo:GFF2791 210 AQNNPHSMGKWSADSKTKVSSMLGNDFYANEVSATISAAQagTAKIEFVGKDGAVTVLKDSWPLEEGTVADATFMS 285
                                        ************************************98762269******************************** PP

                          TIGR00178 231 kkalvefleeeiedakeegvllslhlkatmmkvsdpivfGhvvrvfykdvfakhaelleqlGldvenGladlyaki 306
                                        +kal+ fl++ ied+k++g ++slh+katmmkvsdpi+fGh+v+++   v+ k+++ +e++G  ++ Gl++++a i
  lcl|FitnessBrowser__Phaeo:GFF2791 286 AKALSSFLKDAIEDTKADGTMFSLHMKATMMKVSDPIIFGHAVKAWLGPVWDKFGAEIEAAGGSANSGLGAVLATI 361
                                        **************************************************************************** PP

                          TIGR00178 307 eslpaakkeeieadlekvyeerpelamvdsdkGitnlhvpsdvivdasmpamirasGkmygkdgklkdtkavipds 382
                                        + lp++  + i+a++ +   +rp + mvdsdkGitnlhvpsdvi+dasmpa+ira+Gk +++ g++ dt+ vipd+
  lcl|FitnessBrowser__Phaeo:GFF2791 362 DGLPNG--DAIKAEIAAL--DRPSMYMVDSDKGITNLHVPSDVIIDASMPAVIRAGGKGWDEAGNKGDTNCVIPDR 433
                                        ******..99***99875..8******************************************************* PP

                          TIGR00178 383 syagvyqaviedckknGafdpttmGtvpnvGlmaqkaeeyGshdktfeieadGvvrvvdssGevlleeeveagdiw 458
                                        +y+ vy++ i++ k nGa+d tt G+v nvGlmaqkaeeyGsh  tfe +adG++r+v ++Ge l  +eveagdiw
  lcl|FitnessBrowser__Phaeo:GFF2791 434 CYSTVYDESINFFKANGALDVTTAGSVANVGLMAQKAEEYGSHPTTFEAPADGTIRIVLANGETLHAHEVEAGDIW 509
                                        **************************************************************************** PP

                          TIGR00178 459 rmcqvkdapiqdwvklavtrarlsgtpavfwldperahdeelikkvekylkdhdteGldiqilspvkatrfsleri 534
                                        r c vk api++w+ la+ r rl+g  a+fwld++rahd+elik v   l+    + l  qi+ p +at  sl+ i
  lcl|FitnessBrowser__Phaeo:GFF2791 510 RSCTVKKAPIENWIELAMDRQRLTGSEAIFWLDENRAHDAELIKYVTPALEAAGKSDL-FQIMAPREATAQSLKTI 584
                                        **************************************************99998888.7**************** PP

                          TIGR00178 535 rrGedtisvtGnvlrdyltdlfpilelGtsakmlsvvplmaGGGlfetGaGGsapkhvqqleeenhlrwdslGefl 610
                                        + G+d+i++tGnvlrdyltdlfpilelGtsakmls+v lm+GGGlfetGaGGsapkhvqql+eenhlrwds+Gef 
  lcl|FitnessBrowser__Phaeo:GFF2791 585 TAGKDSIAITGNVLRDYLTDLFPILELGTSAKMLSIVKLMNGGGLFETGAGGSAPKHVQQLVEENHLRWDSMGEFC 660
                                        **************************************************************************** PP

                          TIGR00178 611 alaaslehvavktgnekakvladtldaatgklldeekspsrkvGeldnrgskfylakywaqelaaqtedkelaasf 686
                                        al++sl+ +a ++gn+ka vl+ + +aat+ +ld+++spsrkvGe dnr s++++a+ywa++laaq +d+elaa+f
  lcl|FitnessBrowser__Phaeo:GFF2791 661 ALGESLNFLADSKGNAKAGVLGAAAEAATQGILDHNRSPSRKVGEPDNRASHYWFARYWAEALAAQGDDAELAAHF 736
                                        **************************************************************************** PP

                          TIGR00178 687 asvaealtkneekivaelaavqGeavdlgGyyapdtdlttkvlrpsatfnail 739
                                        a++a  l+ +ee i +ela+vqG+avdlgGy+++d  +t +v+rpsat+n i+
  lcl|FitnessBrowser__Phaeo:GFF2791 737 APIAAELAAKEEAILSELAEVQGKAVDLGGYFHADPVKTAAVMRPSATLNGII 789
                                        **************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (744 nodes)
Target sequences:                          1  (790 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 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 12.03
//
[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