Alignments for a candidate for putA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Halomonas desiderata SP1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_086510760.1 BZY95_RS15250 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::ANA3:7023590
         (1064 letters)



>NCBI__GCF_002151265.1:WP_086510760.1
          Length = 1063

 Score = 1240 bits (3209), Expect = 0.0
 Identities = 631/1064 (59%), Positives = 797/1064 (74%), Gaps = 10/1064 (0%)

Query: 6    MFKASEVLAGRYDSANLDELFKAVTDNYIVDEEQYLSELIKLVPSSDEAIERVTRRAHEL 65
            M  A  +L       +LD LF  ++++Y+VDEE ++ EL+ ++ ++ E   R+  +  EL
Sbjct: 1    MLNAETMLDAATWQQDLDSLFSRISEHYVVDEETFVKELVNVLSANPEDFRRIADKTAEL 60

Query: 66   VNKVRQFDKKGLMVGIDAFLQQYSLETQEGIILMCLAEALLRIPDAATADALIEDKLSGA 125
            V +VR  D    +  ID  LQQYSL+T EG++LMCLAEA+LRIPD ATADALIEDKL  A
Sbjct: 61   VREVRDMDTA--VDTIDQLLQQYSLDTHEGLMLMCLAEAMLRIPDTATADALIEDKLGPA 118

Query: 126  KWDEHLSKSDSVLVNASTWGLMLTGKIVKLDKKIDGTPSNLLSRLVNRLGEPVIRQAMMA 185
             W  H+ +SDS LVNASTWGL++TG +V LDK  DG PS  ++RLVNR+GEPVIR+AM  
Sbjct: 119  DWKAHVGQSDSWLVNASTWGLLMTGHVVTLDKPRDGKPSGFINRLVNRMGEPVIRRAMYE 178

Query: 186  AMKIMGKQFVLGRTMKEALKNSEDKRKLGYTHSYDMLGEAALTRKDAEKYFNDYANAITE 245
            AMKIMGKQFVLGR + EALK S      GYT+SYDMLGEAA TR DA++YF+DYA AI +
Sbjct: 179  AMKIMGKQFVLGRDIDEALKRSRPLFDKGYTYSYDMLGEAARTRADAKRYFDDYAKAIRQ 238

Query: 246  LGAQSYNENE-SPRPTISIKLSALHPRYEVANEDRVLTELYDTVIRLIKLARGLNIGISI 304
            +G  S    E +P P++SIKLSALHPRYE    +++L EL  +V  L+ +AR  ++ ++I
Sbjct: 239  VGLTSTKLTERTPAPSVSIKLSALHPRYEFGRREQILHELVGSVRELVTMARERDVALTI 298

Query: 305  DAEEVDRLELSLKLFQKLFNADATKGWGLLGIVVQAYSKRALPVLVWLTRLAKEQGDEIP 364
            DAEEVDRLELSL++F+ ++ ++A KGWG  G+VVQAYSKRALPVL +L RLA  QGDEIP
Sbjct: 299  DAEEVDRLELSLEVFRAVYESEACKGWGHFGLVVQAYSKRALPVLHYLNRLADRQGDEIP 358

Query: 365  VRLVKGAYWDSELKWAQQAGEAAYPLYTRKAGTDVSYLACARYLLSDATRGAIYPQFASH 424
            VRLVKGAYWDSE+K +QQ G   YP+YTRKA TDV+YL CAR+LLSD TRG I+PQFA+H
Sbjct: 359  VRLVKGAYWDSEIKESQQLGVEGYPVYTRKACTDVAYLVCARFLLSDQTRGRIFPQFATH 418

Query: 425  NAQTVAAISDMAGD--RNHEFQRLHGMGQELYDTILSEAGAKAV-RIYAPIGAHKDLLPY 481
            NA T++ I +MA +  R  EFQRLHGMG+ LYD  L  A      RIYAP+GAHKDLLPY
Sbjct: 419  NAHTISTILEMADEATRPFEFQRLHGMGEALYDAALKRAPKGTYCRIYAPVGAHKDLLPY 478

Query: 482  LVRRLLENGANTSFVHKLVDPKTPIESLVVHPLKTLTGYKTLANNKIVLPTDIFGSDRKN 541
            LVRRLLENGAN+SFVH+LVDPK P+E+L VHP++TL  Y+T +N +I LP DI+G  R+N
Sbjct: 479  LVRRLLENGANSSFVHQLVDPKVPVETLCVHPVETLGQYRTFSNPRIPLPKDIYGERRRN 538

Query: 542  SKGLNMNIISEAEPFFAALDKFKSTQWQAGPLV--NGQTLTGEHKTVVSPFDTTQTVGQV 599
            S+G+N+N+ S  EP   A+  F    ++ GPL+  + + + G    V SP+D  Q VG V
Sbjct: 539  SRGVNLNVRSHYEPLMKAMSGFMERSYEVGPLLAFDVERIAGNVHEVFSPYDRRQRVGSV 598

Query: 600  AFADKAAIEQAVASADAAFATWTRTPVEVRASALQKLADLLEENREELIALCTREAGKSI 659
             +  +    +AV +A AAF  W  TPV  RA+ +++L DL+EEN  EL+ LC+RE GK +
Sbjct: 599  QWTTRDQAARAVDAAWAAFPRWEATPVAERAAIIRRLGDLMEENLAELMTLCSREGGKLL 658

Query: 660  QDGIDEVREAVDFCRYYAVQAKKLMSKPELLPGPTGELNELFLQGRGVFVCISPWNFPLA 719
             DG+DE+REAVDFCRYYA++A++   +P  LPGPTGE N L L G+GVF  ISPWNFP+A
Sbjct: 659  TDGVDEIREAVDFCRYYAMRAEEQFGEPLELPGPTGESNRLMLSGKGVFAAISPWNFPVA 718

Query: 720  IFLGQVSAALAAGNTVVAKPAEQTSIIGYRAVQLAHQAGIPTDVLQYLPGTGATVGNALT 779
            IF GQV AA  AGN+V+AKPAEQTSI+ +R ++L H+AG+P DV+Q LPG G TVG+ LT
Sbjct: 719  IFCGQVVAAAVAGNSVLAKPAEQTSIVAHRVIELLHEAGMPRDVVQLLPGDGPTVGSVLT 778

Query: 780  ADERIGGVCFTGSTGTAKLINRTLANREGAIIP-LIAETGGQNAMVVDSTSQPEQVVNDV 838
            +D RI GV FTG T TA++INR LA RE A +P L+AETGG NA++VDST+ PEQVV DV
Sbjct: 779  SDPRITGVAFTGGTDTAQIINRALAARENAPLPALVAETGGMNALIVDSTALPEQVVADV 838

Query: 839  VSSSFTSAGQRCSALRVLFLQEDIADRVIDVLQGAMDELVIGNPSSVKTDVGPVIDATAK 898
            + S++ SAGQRCSALRVL+LQED+ADRVI++L+GAMDEL +G+P  + TDVGPVID  A+
Sbjct: 839  IQSAYQSAGQRCSALRVLYLQEDVADRVIEILRGAMDELHVGDPRDLGTDVGPVIDEDAR 898

Query: 899  ANLDAHIDHIKQVGKLIKQMSL-PAGTENGHFVSPTAVEIDSIKVLEKEHFGPILHVIRY 957
             NL AHI+ +K  G+L+ +  L PA T +G FV P A  ID+I  LE+E FGP+LHV+RY
Sbjct: 899  KNLLAHIEKLKGEGRLLAETRLDPAHTAHGTFVPPVAFSIDAIDALEREQFGPVLHVVRY 958

Query: 958  KASELAHVIDEINSTGFGLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFG 1017
            KASE+  V+D IN+ G+GLT G+HSRNE  A  VA K+ VGNVYINRN IGAVVGVQPFG
Sbjct: 959  KASEIEQVLDSINARGYGLTFGVHSRNESFAQLVAQKIRVGNVYINRNIIGAVVGVQPFG 1018

Query: 1018 GQGLSGTGPKAGGPHYLTRFVTEKTRTNNITAIGGNATLLSLGD 1061
            GQGLSGTGPKAGGPHYL RF TEKT T N  A+GGNA+LL+LGD
Sbjct: 1019 GQGLSGTGPKAGGPHYLLRFATEKTVTVNTAALGGNASLLALGD 1062


Lambda     K      H
   0.317    0.133    0.377 

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: 2635
Number of extensions: 95
Number of successful extensions: 8
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: 1064
Length of database: 1063
Length adjustment: 45
Effective length of query: 1019
Effective length of database: 1018
Effective search space:  1037342
Effective search space used:  1037342
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 (21.6 bits)
S2: 58 (26.9 bits)

Align candidate WP_086510760.1 BZY95_RS15250 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01238.hmm
# target sequence database:        /tmp/gapView.18797.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-216  706.0   0.0   1.6e-216  705.5   0.0    1.1  1  lcl|NCBI__GCF_002151265.1:WP_086510760.1  BZY95_RS15250 bifunctional proli


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510760.1  BZY95_RS15250 bifunctional proline dehydrogenase/L-glutamate gamma-semialde
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  705.5   0.0  1.6e-216  1.6e-216       1     497 [.     530    1040 ..     530    1043 .. 0.98

  Alignments for each domain:
  == domain 1  score: 705.5 bits;  conditional E-value: 1.6e-216
                                 TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivg.ekakaegeaqpvknpadrkdivG 66  
                                                d+yge r+ns Gv+l++ s+ ++l + +   ++++++  p+++ +  +  g+++ v +p+dr++ vG
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  530 DIYGERRRNSRGVNLNVRSHYEPLMKAMSGFMERSYEVGPLLAfDVERIAGNVHEVFSPYDRRQRVG 596 
                                                89****************************************9888899****************** PP

                                 TIGR01238   67 qvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaia 133 
                                                 v+ +  +++ +avd+a aaf+ w+at+ +eraai++rl dl+e+++ el++l+ re Gk l + ++
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  597 SVQWTTRDQAARAVDAAWAAFPRWEATPVAERAAIIRRLGDLMEENLAELMTLCSREGGKLLTDGVD 663 
                                                ******************************************************************* PP

                                 TIGR01238  134 evreavdflryyakqvedvldeesaka.............lGavvcispwnfplaiftGqiaaalaa 187 
                                                e+reavdf+ryya ++e++++e    +             +G++ +ispwnfp+aif Gq++aa +a
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  664 EIREAVDFCRYYAMRAEEQFGEPLELPgptgesnrlmlsgKGVFAAISPWNFPVAIFCGQVVAAAVA 730 
                                                *********************997777999999********************************** PP

                                 TIGR01238  188 GntviakpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarl 254 
                                                Gn+v+akpaeqts++a r +ell+eaG+p  v+qllpG G +vG+ ltsd+ri+Gv+ftG t++a+ 
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  731 GNSVLAKPAEQTSIVAHRVIELLHEAGMPRDVVQLLPGDGPTVGSVLTSDPRITGVAFTGGTDTAQI 797 
                                                ******************************************************************* PP

                                 TIGR01238  255 inkalakredap.vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqedvad 320 
                                                in+ala re+ap  +l+aetGG+na+ivdstal+eqvvadv++sa++saGqrcsalrvl++qedvad
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  798 INRALAARENAPlPALVAETGGMNALIVDSTALPEQVVADVIQSAYQSAGQRCSALRVLYLQEDVAD 864 
                                                ************4469*************************************************** PP

                                 TIGR01238  321 rvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddvesekgtf 387 
                                                rv+++++Gamdel+vg p  l tdvGpvid++a++nllahiek+k+ ++ +a+ +l+   ++ +gtf
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  865 RVIEILRGAMDELHVGDPRDLGTDVGPVIDEDARKNLLAHIEKLKGEGRLLAETRLDP-AHTAHGTF 930 
                                                *****************************************************99998.8999**** PP

                                 TIGR01238  388 vaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieetvrqiekrak 454 
                                                v+p++f +d +d+l++e+fGpvlhvvryka+e+++v+d ina+Gyglt+Gvhsr+e+  + + ++++
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  931 VPPVAFSIDAIDALEREQFGPVLHVVRYKASEIEQVLDSINARGYGLTFGVHSRNESFAQLVAQKIR 997 
                                                ******************************************************************* PP

                                 TIGR01238  455 vGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497 
                                                vGnvy+nrn++GavvGvqpfGG+GlsGtGpkaGGp+yl r+  
  lcl|NCBI__GCF_002151265.1:WP_086510760.1  998 VGNVYINRNIIGAVVGVQPFGGQGLSGTGPKAGGPHYLLRFAT 1040
                                                ****************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1063 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 20.93
//
[ok]

This GapMind analysis is from Sep 24 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources