GapMind for catabolism of small carbon sources

 

Alignments for a candidate for put1 in Phaeobacter inhibens BS107

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate GFF1160 PGA1_c11750 bifunctional protein PutA

Query= reanno::Phaeo:GFF1160
         (1158 letters)



>FitnessBrowser__Phaeo:GFF1160
          Length = 1158

 Score = 2282 bits (5914), Expect = 0.0
 Identities = 1158/1158 (100%), Positives = 1158/1158 (100%)

Query: 1    MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN 60
            MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN
Sbjct: 1    MTAPQSKTTPEMPSAPTPEYSDALRYRIDAGTYVDQAQMRDQLFALANLDATDRSTISAN 60

Query: 61   AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP 120
            AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP
Sbjct: 61   AAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVALMCLAEALLRVPDADTIDALIEDKIAP 120

Query: 121  SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK 180
            SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK
Sbjct: 121  SEWGKHLGKSTSSLVNASTWALMLTGKVLDEKRSPVSALRGAMKRLGEPVIRTAVSRAMK 180

Query: 181  EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA 240
            EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA
Sbjct: 181  EMGRQFVLGETIEGAMKRAAGMEAKGYTYSYDMLGEAARTEADAARYHLAYSRAISAIAA 240

Query: 241  ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE 300
            ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE
Sbjct: 241  ACNSADIRQNPGISVKLSALHPRYELAQETSVKEQLVPRLQALALLAKAAGMGLNVDAEE 300

Query: 301  ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV 360
            ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV
Sbjct: 301  ADRLSLSLEVIEEVISDPALAGWDGFGVVVQAYGPRTGAALDALYDMANRYDRRLMVRLV 360

Query: 361  KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS 420
            KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS
Sbjct: 361  KGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVSYIANARKLLSITDRIYPQFATHNAHTVS 420

Query: 421  AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE 480
            AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE
Sbjct: 421  AILHMAKDTDKGAYEFQRLHGMGETLHNMVLEQNQTHCRIYAPVGAHRDLLAYLVRRLLE 480

Query: 481  NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT 540
            NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT
Sbjct: 481  NGANSSFVNQIVDENVPPELVAADPFAQVEDLTANLRKGPDLFQPERPNSIGFDLGHAPT 540

Query: 541  LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL 600
            LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL
Sbjct: 541  LAAIDAARAPWKSHSWAAEPLLAKAPETATTTDEPVRNPADLTTVGRVQTAGQAEIETAL 600

Query: 601  SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY 660
            SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY
Sbjct: 601  SAATPWNASAETRAEVLNRAADLYEANYGELFALLTREAGKTLPDCVAELREAVDFLRYY 660

Query: 661  AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH 720
            AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH
Sbjct: 661  AARISAEPPVGVFTCISPWNFPLAIFSGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLH 720

Query: 721  EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE 780
            EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE
Sbjct: 721  EAGVPRSALQLLPGAGAVGGALTSDARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAE 780

Query: 781  TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA 840
            TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA
Sbjct: 781  TGGLNAMIVDSTALPEQAVQSIIESAFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDA 840

Query: 841  LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG 900
            LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG
Sbjct: 841  LHLGDPWNLSTDSGPVIDETARAGILAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITG 900

Query: 901  IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN 960
            IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN
Sbjct: 901  IQALEQEIFGPVLHVVRFKSQDLDQIIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGN 960

Query: 961  LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML 1020
            LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML
Sbjct: 961  LYVNRNQIGAIVGSQPFGGEGLSGTGPKAGGPFYMMRFCAPDRQKSVDSWPSDAPAMTML 1020

Query: 1021 PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA 1080
            PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA
Sbjct: 1021 PAPTGQPMQEITTSLPGPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEA 1080

Query: 1081 TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV 1140
            TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV
Sbjct: 1081 TGPLDMRQLLTMEGTSGVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHV 1140

Query: 1141 CVDTTAAGGNAALLGGMG 1158
            CVDTTAAGGNAALLGGMG
Sbjct: 1141 CVDTTAAGGNAALLGGMG 1158


Lambda     K      H
   0.317    0.132    0.387 

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: 3626
Number of extensions: 133
Number of successful extensions: 1
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: 1158
Length of database: 1158
Length adjustment: 47
Effective length of query: 1111
Effective length of database: 1111
Effective search space:  1234321
Effective search space used:  1234321
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 (21.7 bits)
S2: 58 (26.9 bits)

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