Alignments for a candidate for gdhA in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for gdhA in Caulobacter crescentus NA1000

Align glutamate dehydrogenase (EC 1.4.1.2) (characterized)
to candidate CCNA_00086 CCNA_00086 NAD-specific glutamate dehydrogenase GdhZ

Query= BRENDA::A0A0H3C571
         (1607 letters)



>FitnessBrowser__Caulo:CCNA_00086
          Length = 1607

 Score = 3136 bits (8131), Expect = 0.0
 Identities = 1607/1607 (100%), Positives = 1607/1607 (100%)

Query: 1    MSGVKIDPSNSLTAAYALTRGKTVQELALEERDFLAQVGADWAIEDAPVLSAKAAAASLA 60
            MSGVKIDPSNSLTAAYALTRGKTVQELALEERDFLAQVGADWAIEDAPVLSAKAAAASLA
Sbjct: 1    MSGVKIDPSNSLTAAYALTRGKTVQELALEERDFLAQVGADWAIEDAPVLSAKAAAASLA 60

Query: 61   EFFDFARTLKGDQPTVRLRSAGEAGAARDLLEIVQPDRPFLVDSVMGEITESGFRVRAMF 120
            EFFDFARTLKGDQPTVRLRSAGEAGAARDLLEIVQPDRPFLVDSVMGEITESGFRVRAMF
Sbjct: 61   EFFDFARTLKGDQPTVRLRSAGEAGAARDLLEIVQPDRPFLVDSVMGEITESGFRVRAMF 120

Query: 121  HPVVEIDGIARSFIQVHLDPVGEDRVESLLEQIRETLFDVRRAVGDFKAMRDLMHRAVAE 180
            HPVVEIDGIARSFIQVHLDPVGEDRVESLLEQIRETLFDVRRAVGDFKAMRDLMHRAVAE
Sbjct: 121  HPVVEIDGIARSFIQVHLDPVGEDRVESLLEQIRETLFDVRRAVGDFKAMRDLMHRAVAE 180

Query: 181  LAATPGVTSEEGRQEDLAFLRWLEDDNFVFLGARVYEYPRSSDGGYAAEEPLYEAEASLG 240
            LAATPGVTSEEGRQEDLAFLRWLEDDNFVFLGARVYEYPRSSDGGYAAEEPLYEAEASLG
Sbjct: 181  LAATPGVTSEEGRQEDLAFLRWLEDDNFVFLGARVYEYPRSSDGGYAAEEPLYEAEASLG 240

Query: 241  VLRDSSRSVLRRAYEPAILSKQLQRQLETGAPVVVAKSNLRSRVHRRGFMDYVGVRRYGD 300
            VLRDSSRSVLRRAYEPAILSKQLQRQLETGAPVVVAKSNLRSRVHRRGFMDYVGVRRYGD
Sbjct: 241  VLRDSSRSVLRRAYEPAILSKQLQRQLETGAPVVVAKSNLRSRVHRRGFMDYVGVRRYGD 300

Query: 301  DGKPSGEVRFVGLFTAEAYETPAVEVPLIRHRVARIMRRAAKAPGSHNEKRLRNILETWP 360
            DGKPSGEVRFVGLFTAEAYETPAVEVPLIRHRVARIMRRAAKAPGSHNEKRLRNILETWP
Sbjct: 301  DGKPSGEVRFVGLFTAEAYETPAVEVPLIRHRVARIMRRAAKAPGSHNEKRLRNILETWP 360

Query: 361  RDELFQTSEDTLLSMALGVLHLIDRPRVRLFARLDPFDRFASVLVYIPRERFDTEVCARA 420
            RDELFQTSEDTLLSMALGVLHLIDRPRVRLFARLDPFDRFASVLVYIPRERFDTEVCARA
Sbjct: 361  RDELFQTSEDTLLSMALGVLHLIDRPRVRLFARLDPFDRFASVLVYIPRERFDTEVCARA 420

Query: 421  GAILADAYDGKVLEYYPEISDAPLARAHFIIEVTPGDHPDPDLSQVEARIADTALTWEDR 480
            GAILADAYDGKVLEYYPEISDAPLARAHFIIEVTPGDHPDPDLSQVEARIADTALTWEDR
Sbjct: 421  GAILADAYDGKVLEYYPEISDAPLARAHFIIEVTPGDHPDPDLSQVEARIADTALTWEDR 480

Query: 481  FEAVVRAGGAPTGGVRTLLDKYGYAFPPGYRDQYDALEALADIDIIETLTEGALPRVRAF 540
            FEAVVRAGGAPTGGVRTLLDKYGYAFPPGYRDQYDALEALADIDIIETLTEGALPRVRAF
Sbjct: 481  FEAVVRAGGAPTGGVRTLLDKYGYAFPPGYRDQYDALEALADIDIIETLTEGALPRVRAF 540

Query: 541  RRFEDGPRTFRFKLYLRGAAAPLAEVLPILERMGLKALIEDGFRLSIHEKDGPHSVWVHE 600
            RRFEDGPRTFRFKLYLRGAAAPLAEVLPILERMGLKALIEDGFRLSIHEKDGPHSVWVHE
Sbjct: 541  RRFEDGPRTFRFKLYLRGAAAPLAEVLPILERMGLKALIEDGFRLSIHEKDGPHSVWVHE 600

Query: 601  FVLDDPAGEHIVFDEVRQVFEEAFIAIWTGATENDGFNRIVLEMAVGWREAALLRALARY 660
            FVLDDPAGEHIVFDEVRQVFEEAFIAIWTGATENDGFNRIVLEMAVGWREAALLRALARY
Sbjct: 601  FVLDDPAGEHIVFDEVRQVFEEAFIAIWTGATENDGFNRIVLEMAVGWREAALLRALARY 660

Query: 661  RQQSGLDPSQQVQEAALRDHPMVARLILDLFRVKFDPAIRADLRTRREQAEAVQFSIVEA 720
            RQQSGLDPSQQVQEAALRDHPMVARLILDLFRVKFDPAIRADLRTRREQAEAVQFSIVEA
Sbjct: 661  RQQSGLDPSQQVQEAALRDHPMVARLILDLFRVKFDPAIRADLRTRREQAEAVQFSIVEA 720

Query: 721  LQAVESLDADRVLRRLAALVGAIQRTNFYQLGADGEPKSYISFKIASRELEDLPAPKPYR 780
            LQAVESLDADRVLRRLAALVGAIQRTNFYQLGADGEPKSYISFKIASRELEDLPAPKPYR
Sbjct: 721  LQAVESLDADRVLRRLAALVGAIQRTNFYQLGADGEPKSYISFKIASRELEDLPAPKPYR 780

Query: 781  EIYVSAPHVEGVHLRFGPVARGGLRWSDRRDDFRTEVLGLVKAQQVKNAVIVPVGSKGGF 840
            EIYVSAPHVEGVHLRFGPVARGGLRWSDRRDDFRTEVLGLVKAQQVKNAVIVPVGSKGGF
Sbjct: 781  EIYVSAPHVEGVHLRFGPVARGGLRWSDRRDDFRTEVLGLVKAQQVKNAVIVPVGSKGGF 840

Query: 841  YPKQLPRGGDRDAIQAEAIRAYKTFLSGLLDLTDNIDSDNQVVPPPSVIAHDAQDPYLVV 900
            YPKQLPRGGDRDAIQAEAIRAYKTFLSGLLDLTDNIDSDNQVVPPPSVIAHDAQDPYLVV
Sbjct: 841  YPKQLPRGGDRDAIQAEAIRAYKTFLSGLLDLTDNIDSDNQVVPPPSVIAHDAQDPYLVV 900

Query: 901  AADKGTATFSDIANGVAESYGFWLGDAFASGGSVGYDHKVMGITARGAWEAVKRHFRELG 960
            AADKGTATFSDIANGVAESYGFWLGDAFASGGSVGYDHKVMGITARGAWEAVKRHFRELG
Sbjct: 901  AADKGTATFSDIANGVAESYGFWLGDAFASGGSVGYDHKVMGITARGAWEAVKRHFRELG 960

Query: 961  KDIQTEAFTVVGVGDMSGDVFGNGMLLSKQTKLLAAFDHRHIFLDPNPDPAVSWAERDRM 1020
            KDIQTEAFTVVGVGDMSGDVFGNGMLLSKQTKLLAAFDHRHIFLDPNPDPAVSWAERDRM
Sbjct: 961  KDIQTEAFTVVGVGDMSGDVFGNGMLLSKQTKLLAAFDHRHIFLDPNPDPAVSWAERDRM 1020

Query: 1021 FKLPRSSWEDYDKSKISAGGGVFARSLKSIPLSAEVRAMLEIKAEAVSPAELMTAILKSK 1080
            FKLPRSSWEDYDKSKISAGGGVFARSLKSIPLSAEVRAMLEIKAEAVSPAELMTAILKSK
Sbjct: 1021 FKLPRSSWEDYDKSKISAGGGVFARSLKSIPLSAEVRAMLEIKAEAVSPAELMTAILKSK 1080

Query: 1081 AELLYLGGIGTYVKAKGETNADAGDKANDAIRINGSDLRVKVVGEGANLGLTQAGRIEFA 1140
            AELLYLGGIGTYVKAKGETNADAGDKANDAIRINGSDLRVKVVGEGANLGLTQAGRIEFA
Sbjct: 1081 AELLYLGGIGTYVKAKGETNADAGDKANDAIRINGSDLRVKVVGEGANLGLTQAGRIEFA 1140

Query: 1141 QAGGHINTDAIDNSAGVDSSDHEVNIKILTGILERGGQLDRESRNTLLASMTDDVAHHVL 1200
            QAGGHINTDAIDNSAGVDSSDHEVNIKILTGILERGGQLDRESRNTLLASMTDDVAHHVL
Sbjct: 1141 QAGGHINTDAIDNSAGVDSSDHEVNIKILTGILERGGQLDRESRNTLLASMTDDVAHHVL 1200

Query: 1201 EHNYDQTLALTLLESDAVSEVDAQIRYMVNLEQRGRLDRRVEGLPTNTTLLERKAAGRGL 1260
            EHNYDQTLALTLLESDAVSEVDAQIRYMVNLEQRGRLDRRVEGLPTNTTLLERKAAGRGL
Sbjct: 1201 EHNYDQTLALTLLESDAVSEVDAQIRYMVNLEQRGRLDRRVEGLPTNTTLLERKAAGRGL 1260

Query: 1261 TRPELAVLLAYGKLDLFDEIVASQSPDDPWFERTLRGYFPRALDQYADAMQKHRLKREII 1320
            TRPELAVLLAYGKLDLFDEIVASQSPDDPWFERTLRGYFPRALDQYADAMQKHRLKREII
Sbjct: 1261 TRPELAVLLAYGKLDLFDEIVASQSPDDPWFERTLRGYFPRALDQYADAMQKHRLKREII 1320

Query: 1321 ATVVGNQMVNMCGPTFVSRLKAAAGADVNAVVVGFTAAREILGIDGLWDQVNGLDNKASA 1380
            ATVVGNQMVNMCGPTFVSRLKAAAGADVNAVVVGFTAAREILGIDGLWDQVNGLDNKASA
Sbjct: 1321 ATVVGNQMVNMCGPTFVSRLKAAAGADVNAVVVGFTAAREILGIDGLWDQVNGLDNKASA 1380

Query: 1381 EGQTALYKALAYALRSLTFWLARRAQRDAANVQTLVEAYGPSVAALKALAPAILSPFEQK 1440
            EGQTALYKALAYALRSLTFWLARRAQRDAANVQTLVEAYGPSVAALKALAPAILSPFEQK
Sbjct: 1381 EGQTALYKALAYALRSLTFWLARRAQRDAANVQTLVEAYGPSVAALKALAPAILSPFEQK 1440

Query: 1441 AVSKRVKAYVADGAPEALALSVAALQPLTTAADLVDLANASSWSVENVARLYHQVGAAFG 1500
            AVSKRVKAYVADGAPEALALSVAALQPLTTAADLVDLANASSWSVENVARLYHQVGAAFG
Sbjct: 1441 AVSKRVKAYVADGAPEALALSVAALQPLTTAADLVDLANASSWSVENVARLYHQVGAAFG 1500

Query: 1501 FDRLRGAAGSFVGGDAFERLAVRRLIEDMLTEQTSITQQVLKFAANAQAGEDEAAAKAAI 1560
            FDRLRGAAGSFVGGDAFERLAVRRLIEDMLTEQTSITQQVLKFAANAQAGEDEAAAKAAI
Sbjct: 1501 FDRLRGAAGSFVGGDAFERLAVRRLIEDMLTEQTSITQQVLKFAANAQAGEDEAAAKAAI 1560

Query: 1561 SSWAALRGDRPRAVKRTIEDIEQAGGGWTFAKLTIANAALRELSSAA 1607
            SSWAALRGDRPRAVKRTIEDIEQAGGGWTFAKLTIANAALRELSSAA
Sbjct: 1561 SSWAALRGDRPRAVKRTIEDIEQAGGGWTFAKLTIANAALRELSSAA 1607


Lambda     K      H
   0.319    0.135    0.390 

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: 6987
Number of extensions: 289
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: 1607
Length of database: 1607
Length adjustment: 51
Effective length of query: 1556
Effective length of database: 1556
Effective search space:  2421136
Effective search space used:  2421136
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: 61 (28.1 bits)

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

Downloads

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

Related tools

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