Alignments for a candidate for put1 in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for put1 in Acidovorax sp. GW101-3H11

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Ac3H11_2850 Transcriptional repressor of PutA and PutP / Proline dehydrogenase (EC 1.5.99.8) (Proline oxidase) / Delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)

Query= reanno::acidovorax_3H11:Ac3H11_2850
         (1261 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2850
          Length = 1261

 Score = 2471 bits (6405), Expect = 0.0
 Identities = 1261/1261 (100%), Positives = 1261/1261 (100%)

Query: 1    MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60
            MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ
Sbjct: 1    MTLPTAPFADFAPRTPLANPLRAAITAAITAATRHPEPEALAPLLAQARLPADQAAAAEQ 60

Query: 61   LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120
            LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR
Sbjct: 61   LALRIAKALRERKASAGRAGIVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIR 120

Query: 121  DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180
            DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK
Sbjct: 121  DKISHGQWDAHLGKSPSLFVNAATWGLLITGKLVATHSEGSLGNSLSRLIGKGGEPLIRK 180

Query: 181  GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240
            GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ
Sbjct: 181  GVDMAMRMMGEQFVTGETIDEALRNARTMEAEGFRYSYDMLGEAALTSEDAKRYYSSYEQ 240

Query: 241  AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300
            AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG
Sbjct: 241  AIHAIGKASAGRGIYEGPGISIKLSALHPRYSRAQFGRVMDELYPLVLRLTALAKQYDIG 300

Query: 301  LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360
            LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR
Sbjct: 301  LNIDAEETDRLELSLDLLERLCHEPTLAGWNGIGFVIQAYQKRCPFVIDCVVDLARRTQR 360

Query: 361  RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420
            RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT
Sbjct: 361  RLMVRLVKGAYWDSEIKRAQVDGLKDYPVYTRKVHTDISYIACAKKLLAAPEAVYPQFAT 420

Query: 421  HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480
            HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC
Sbjct: 421  HNAETVATIYQLAGSNYYAGQYEFQCLHGMGEPLYEQVVGAITAGKLGREIGKGGLGRPC 480

Query: 481  RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540
            RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT
Sbjct: 481  RIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADETIALDELVKSPVQVVDQQAATEGT 540

Query: 541  AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600
            AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA
Sbjct: 541  AGLPHPRIPLPAALYGAHRSNSRGLDLSNENTLTELAATLQATASHAWTAAPLLAADVPA 600

Query: 601  GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660
            GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL
Sbjct: 601  GTTQPVRNPADHNDVVGQVQEATTADVDQALVHAQAAATSWAATPPAERAAALLRTADLL 660

Query: 661  EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720
            EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP
Sbjct: 661  EERIQPLMGLLMREAGKSASNAVAEVREAVDFLRYYAAQVQSTFDNATHIPLGPVACISP 720

Query: 721  WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780
            WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET
Sbjct: 721  WNFPLAIFMGQVAAALAAGNPVLAKPAEQTPLIAAEAVRLLWQAGVPRAAVQLLPGQGET 780

Query: 781  VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840
            VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL
Sbjct: 781  VGARLIGDARVMGVMFTGSTEVARILQRTVAGRLDAAGRPIPLIAETGGQNAMIVDSSAL 840

Query: 841  VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900
            VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG
Sbjct: 841  VEQVVGDAVSSAFDSAGQRCSALRVLCVQEEAADRVVEMLQGAMGELRVGNPGELRVDVG 900

Query: 901  PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960
            PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF
Sbjct: 901  PVIDAEAQAGIAQHIEKFKAQGHRVFQHPNHVSAISAPGTFVPPTLIELNHIGELQREVF 960

Query: 961  GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020
            GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG
Sbjct: 961  GPVLHLVRYARSDLDQLLDQINATGYGLTQGVHTRIDETIARVVNRAHAGNVYVNRNMVG 1020

Query: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080
            AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL
Sbjct: 1021 AVVGVQPFGGEGLSGTGPKAGGPLYLLRLLSQRPADALARTFAEADRTSPHDTERRERHL 1080

Query: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140
            APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH
Sbjct: 1081 APLATLQQWAHNQGNLALAGHCQRFAQETQSGTSRTLPGPTGERNVYTLAPRARVLCLAH 1140

Query: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200
            SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH
Sbjct: 1141 SVDDLLVQTAAVLASGGTALWPHAHAGLRAKLPTHVQAQVMLQDNTLSDGSVALDAVLHH 1200

Query: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260
            GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI
Sbjct: 1201 GDAPSLQAVCTTLARRPGPIVGVTALQPGAADIPLERLLIERALSVNTAAAGGNASLMTI 1260

Query: 1261 G 1261
            G
Sbjct: 1261 G 1261


Lambda     K      H
   0.318    0.133    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: 4343
Number of extensions: 160
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: 1261
Length of database: 1261
Length adjustment: 48
Effective length of query: 1213
Effective length of database: 1213
Effective search space:  1471369
Effective search space used:  1471369
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: 59 (27.3 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