Alignments for a candidate for gdhA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Pseudomonas stutzeri RCH2

Align NAD-specific glutamate dehydrogenase (EC 1.4.1.2), large form (characterized)
to candidate GFF1903 Psest_1944 NAD-specific glutamate dehydrogenase

Query= reanno::psRCH2:GFF1903
         (1616 letters)



>FitnessBrowser__psRCH2:GFF1903
          Length = 1616

 Score = 3180 bits (8244), Expect = 0.0
 Identities = 1616/1616 (100%), Positives = 1616/1616 (100%)

Query: 1    MAFFSAASKADFQQQLQTALAQHVDSKILPQLNLFAEQFFGIVALPELTERRMSDLVGST 60
            MAFFSAASKADFQQQLQTALAQHVDSKILPQLNLFAEQFFGIVALPELTERRMSDLVGST
Sbjct: 1    MAFFSAASKADFQQQLQTALAQHVDSKILPQLNLFAEQFFGIVALPELTERRMSDLVGST 60

Query: 61   LASWRLLERFEPSTPEVQVFNPDFEKHGWQSTHSVVEVLHPDMPFLVDSVRMELTRRGYS 120
            LASWRLLERFEPSTPEVQVFNPDFEKHGWQSTHSVVEVLHPDMPFLVDSVRMELTRRGYS
Sbjct: 61   LASWRLLERFEPSTPEVQVFNPDFEKHGWQSTHSVVEVLHPDMPFLVDSVRMELTRRGYS 120

Query: 121  IHTLQTSVLQVRRAADGSLLELLPKDERAADSHAESLIFVEIDRCASPSALRELEQSLLG 180
            IHTLQTSVLQVRRAADGSLLELLPKDERAADSHAESLIFVEIDRCASPSALRELEQSLLG
Sbjct: 121  IHTLQTSVLQVRRAADGSLLELLPKDERAADSHAESLIFVEIDRCASPSALRELEQSLLG 180

Query: 181  VLADVRQVVGDFAAMKGKAVELQGRLEQVNLSIDGDELDEIRDFMRWLADDHFTFLGYEE 240
            VLADVRQVVGDFAAMKGKAVELQGRLEQVNLSIDGDELDEIRDFMRWLADDHFTFLGYEE
Sbjct: 181  VLADVRQVVGDFAAMKGKAVELQGRLEQVNLSIDGDELDEIRDFMRWLADDHFTFLGYEE 240

Query: 241  FSVQEQADGGRIFYDESSLLGLSRTMRTGLSEEEQSLTAQSMSYLREPLLLSFAKAAMPS 300
            FSVQEQADGGRIFYDESSLLGLSRTMRTGLSEEEQSLTAQSMSYLREPLLLSFAKAAMPS
Sbjct: 241  FSVQEQADGGRIFYDESSLLGLSRTMRTGLSEEEQSLTAQSMSYLREPLLLSFAKAAMPS 300

Query: 301  RVHRPAYPDFVSVREFDEAGRVVRECRFLGLFTSSVYTQSVRRIPFIRRKVETVVQRANF 360
            RVHRPAYPDFVSVREFDEAGRVVRECRFLGLFTSSVYTQSVRRIPFIRRKVETVVQRANF
Sbjct: 301  RVHRPAYPDFVSVREFDEAGRVVRECRFLGLFTSSVYTQSVRRIPFIRRKVETVVQRANF 360

Query: 361  GSSAHLAKELVQVLEVLPRDELFQAPIDELFENAIAIVQIQERNRLRLFLRFDPYRRFCY 420
            GSSAHLAKELVQVLEVLPRDELFQAPIDELFENAIAIVQIQERNRLRLFLRFDPYRRFCY
Sbjct: 361  GSSAHLAKELVQVLEVLPRDELFQAPIDELFENAIAIVQIQERNRLRLFLRFDPYRRFCY 420

Query: 421  CLVYVPRDSYSTETRLKIQQVLQERLEASDCEFSTYFSESVLTRVQFILRLDPSRAVQVD 480
            CLVYVPRDSYSTETRLKIQQVLQERLEASDCEFSTYFSESVLTRVQFILRLDPSRAVQVD
Sbjct: 421  CLVYVPRDSYSTETRLKIQQVLQERLEASDCEFSTYFSESVLTRVQFILRLDPSRAVQVD 480

Query: 481  PVRLEQEVLQACRTWQDDYQSLVVERFGEAKGTHLLSEFPKGFPAGYRERFSPQSATVDM 540
            PVRLEQEVLQACRTWQDDYQSLVVERFGEAKGTHLLSEFPKGFPAGYRERFSPQSATVDM
Sbjct: 481  PVRLEQEVLQACRTWQDDYQSLVVERFGEAKGTHLLSEFPKGFPAGYRERFSPQSATVDM 540

Query: 541  QHVLDLSEERPLVMSFYQPITAEENRLHCKLYHLNTPLPLSDILPIMENLGLRVLGEFPF 600
            QHVLDLSEERPLVMSFYQPITAEENRLHCKLYHLNTPLPLSDILPIMENLGLRVLGEFPF
Sbjct: 541  QHVLDLSEERPLVMSFYQPITAEENRLHCKLYHLNTPLPLSDILPIMENLGLRVLGEFPF 600

Query: 601  RLRNRSGREYWIHDFAFTYAEGLEIDLLEINEALQDAFIHIYGGAAENDAFNRLVLTAGL 660
            RLRNRSGREYWIHDFAFTYAEGLEIDLLEINEALQDAFIHIYGGAAENDAFNRLVLTAGL
Sbjct: 601  RLRNRSGREYWIHDFAFTYAEGLEIDLLEINEALQDAFIHIYGGAAENDAFNRLVLTAGL 660

Query: 661  AWREVALLRAYARYLKQIRMGFDLGYIASALLNHTDIARELVRLFKMRFYLARKLGDEDL 720
            AWREVALLRAYARYLKQIRMGFDLGYIASALLNHTDIARELVRLFKMRFYLARKLGDEDL
Sbjct: 661  AWREVALLRAYARYLKQIRMGFDLGYIASALLNHTDIARELVRLFKMRFYLARKLGDEDL 720

Query: 721  ADKQQRLEQAILSALDDVAVLNEDRILRRYLALIQATLRTNFYQPDANGRPKPYFSFKLD 780
            ADKQQRLEQAILSALDDVAVLNEDRILRRYLALIQATLRTNFYQPDANGRPKPYFSFKLD
Sbjct: 721  ADKQQRLEQAILSALDDVAVLNEDRILRRYLALIQATLRTNFYQPDANGRPKPYFSFKLD 780

Query: 781  PRAIPEMPRPAPMYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDYRTEVLGLVKAQQV 840
            PRAIPEMPRPAPMYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDYRTEVLGLVKAQQV
Sbjct: 781  PRAIPEMPRPAPMYEIFVYSPRVEGVHLRGGKVARGGLRWSDREEDYRTEVLGLVKAQQV 840

Query: 841  KNAVIVPGGAKGGFVPRRLPTTGTRDDIQAEAIACYRIFISGLLDITDNLREGQVAPPAN 900
            KNAVIVPGGAKGGFVPRRLPTTGTRDDIQAEAIACYRIFISGLLDITDNLREGQVAPPAN
Sbjct: 841  KNAVIVPGGAKGGFVPRRLPTTGTRDDIQAEAIACYRIFISGLLDITDNLREGQVAPPAN 900

Query: 901  VLRYDGDDPYLVVAADKGTASFSDIANGIAAEYDFWLGDAFASGGSAGYDHKKMGITARG 960
            VLRYDGDDPYLVVAADKGTASFSDIANGIAAEYDFWLGDAFASGGSAGYDHKKMGITARG
Sbjct: 901  VLRYDGDDPYLVVAADKGTASFSDIANGIAAEYDFWLGDAFASGGSAGYDHKKMGITARG 960

Query: 961  AWVSVQRHFRERGINVQSDVISVIGIGDMAGDVFGNGLLMSETLQLVAAFNHLHIFIDPN 1020
            AWVSVQRHFRERGINVQSDVISVIGIGDMAGDVFGNGLLMSETLQLVAAFNHLHIFIDPN
Sbjct: 961  AWVSVQRHFRERGINVQSDVISVIGIGDMAGDVFGNGLLMSETLQLVAAFNHLHIFIDPN 1020

Query: 1021 PDPARSFLERKRLFDLPRSSWTDYDASLISEGGGIFPRSAKRVQISPQMKERFAIEADQL 1080
            PDPARSFLERKRLFDLPRSSWTDYDASLISEGGGIFPRSAKRVQISPQMKERFAIEADQL
Sbjct: 1021 PDPARSFLERKRLFDLPRSSWTDYDASLISEGGGIFPRSAKRVQISPQMKERFAIEADQL 1080

Query: 1081 TPAELINALLKAPVDLLWNGGIGTYVKSSSESHAEVGDKANDAVRVNGAELRAKVVGEGG 1140
            TPAELINALLKAPVDLLWNGGIGTYVKSSSESHAEVGDKANDAVRVNGAELRAKVVGEGG
Sbjct: 1081 TPAELINALLKAPVDLLWNGGIGTYVKSSSESHAEVGDKANDAVRVNGAELRAKVVGEGG 1140

Query: 1141 NLGMTQLGRVEYALHGGSSNTDFIDNAGGVDCSDHEVNIKILLNEVVSAGDMTAKQRNQL 1200
            NLGMTQLGRVEYALHGGSSNTDFIDNAGGVDCSDHEVNIKILLNEVVSAGDMTAKQRNQL
Sbjct: 1141 NLGMTQLGRVEYALHGGSSNTDFIDNAGGVDCSDHEVNIKILLNEVVSAGDMTAKQRNQL 1200

Query: 1201 LFEMTDAVAELVLQNNYKQTQALSQAQHRSRERAAEYVRLINALEAAGQLDRALEFLPSD 1260
            LFEMTDAVAELVLQNNYKQTQALSQAQHRSRERAAEYVRLINALEAAGQLDRALEFLPSD
Sbjct: 1201 LFEMTDAVAELVLQNNYKQTQALSQAQHRSRERAAEYVRLINALEAAGQLDRALEFLPSD 1260

Query: 1261 EALAERASIGKGLTRPELSVLISYSKIELKKALLDSRVPDDDYLAREMDSAFPQQLAEHF 1320
            EALAERASIGKGLTRPELSVLISYSKIELKKALLDSRVPDDDYLAREMDSAFPQQLAEHF
Sbjct: 1261 EALAERASIGKGLTRPELSVLISYSKIELKKALLDSRVPDDDYLAREMDSAFPQQLAEHF 1320

Query: 1321 RAAMLQHRLKREIVATQIANDLVNNMGITFVQRLNEATGMSAANVAGAYVIVRDIFHLPH 1380
            RAAMLQHRLKREIVATQIANDLVNNMGITFVQRLNEATGMSAANVAGAYVIVRDIFHLPH
Sbjct: 1321 RAAMLQHRLKREIVATQIANDLVNNMGITFVQRLNEATGMSAANVAGAYVIVRDIFHLPH 1380

Query: 1381 WFRQIEALDHKVPAELQLSLMDELMRLGRRATRWFLRNRRSELDAARDVAHFGPRVAALG 1440
            WFRQIEALDHKVPAELQLSLMDELMRLGRRATRWFLRNRRSELDAARDVAHFGPRVAALG
Sbjct: 1381 WFRQIEALDHKVPAELQLSLMDELMRLGRRATRWFLRNRRSELDAARDVAHFGPRVAALG 1440

Query: 1441 LKLDELLQGSTRDHWQERYRRYTEAGVPELLARMVAGTNHLYTLLPILEAADETGQVPAQ 1500
            LKLDELLQGSTRDHWQERYRRYTEAGVPELLARMVAGTNHLYTLLPILEAADETGQVPAQ
Sbjct: 1441 LKLDELLQGSTRDHWQERYRRYTEAGVPELLARMVAGTNHLYTLLPILEAADETGQVPAQ 1500

Query: 1501 VAAAYFAVGGALELPWYLHQLTNMPVGNNWQALAREGFRDDLDSQQRSITVSVLQMENGA 1560
            VAAAYFAVGGALELPWYLHQLTNMPVGNNWQALAREGFRDDLDSQQRSITVSVLQMENGA
Sbjct: 1501 VAAAYFAVGGALELPWYLHQLTNMPVGNNWQALAREGFRDDLDSQQRSITVSVLQMENGA 1560

Query: 1561 ESISERVDAWLAQRPVPLARWRSMLAELRNASGNDYAIYAVASRELQGLAQSARHG 1616
            ESISERVDAWLAQRPVPLARWRSMLAELRNASGNDYAIYAVASRELQGLAQSARHG
Sbjct: 1561 ESISERVDAWLAQRPVPLARWRSMLAELRNASGNDYAIYAVASRELQGLAQSARHG 1616


Lambda     K      H
   0.321    0.136    0.396 

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: 6782
Number of extensions: 221
Number of successful extensions: 5
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: 1616
Length of database: 1616
Length adjustment: 51
Effective length of query: 1565
Effective length of database: 1565
Effective search space:  2449225
Effective search space used:  2449225
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 (21.9 bits)
S2: 61 (28.1 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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