Aligments for a candidate for uxaA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Aligments for a candidate for uxaA in Pedobacter sp. GW460-11-11-14-LB5

Align Altronate dehydratase (EC 4.2.1.7) (characterized)
to candidate CA265_RS19875 CA265_RS19875 altronate hydrolase

Query= reanno::Pedo557:CA265_RS19875
         (548 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS19875 CA265_RS19875 altronate
           hydrolase
          Length = 548

 Score = 1108 bits (2865), Expect = 0.0
 Identities = 548/548 (100%), Positives = 548/548 (100%)

Query: 1   MVTRILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMY 60
           MVTRILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMY
Sbjct: 1   MVTRILKIHPNDNVLVALQNLAKGETVIYDGHEYILQDDIQAKHKFFMQDMNAGDHIIMY 60

Query: 61  GVLVGKAQHFILKGGLMDTENTKHASDPYEFRPYHYEWHAPDVSKFEGRTFNGYIRSDGR 120
           GVLVGKAQHFILKGGLMDTENTKHASDPYEFRPYHYEWHAPDVSKFEGRTFNGYIRSDGR
Sbjct: 61  GVLVGKAQHFILKGGLMDTENTKHASDPYEFRPYHYEWHAPDVSKFEGRTFNGYIRSDGR 120

Query: 121 VGTANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEAD 180
           VGTANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEAD
Sbjct: 121 VGTANYWLFIPTVFCENRNLDVIREALHNELGYAVTDKYKSYAHQLVEAYKNGEILAEAD 180

Query: 181 PSSIGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLS 240
           PSSIGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLS
Sbjct: 181 PSSIGLANPSANRVFKNVDGIKFLNHQGGCGGTRQDAAVLSKLLAAYADHPNVAGVTVLS 240

Query: 241 LGCQNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIER 300
           LGCQNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIER
Sbjct: 241 LGCQNLQVKDFMDDLKHRSPNFDKPLFVFEQQQSQSEEQLVKEAIRKTFIGLTEINKIER 300

Query: 301 QPAPLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLID 360
           QPAPLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLID
Sbjct: 301 QPAPLSKLVLGVKCGGSDGFSGISANPAVGYTSDLLVALGGTVLLAEFPELCGAEQQLID 360

Query: 361 RTKDETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSP 420
           RTKDETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSP
Sbjct: 361 RTKDETAARKFIQLMTAYNQSAENVGSGFFMNPSPGNIKDGLITDAIKSTGAAKKGGTSP 420

Query: 421 VEDVLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKV 480
           VEDVLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKV
Sbjct: 421 VEDVLDYTEPATKPGLNLVCTPGNDVEATTGKAASGATLILFTTGLGTPTGNPVCPTIKV 480

Query: 481 STNNALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFI 540
           STNNALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFI
Sbjct: 481 STNNALTKRMGDIIDINCGPVIEGEKTIEQMGEDILEYCIKAASGEVIPKAVLLNQDDFI 540

Query: 541 PWKRGVSL 548
           PWKRGVSL
Sbjct: 541 PWKRGVSL 548


Lambda     K      H
   0.317    0.136    0.400 

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: 1129
Number of extensions: 38
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: 548
Length of database: 548
Length adjustment: 36
Effective length of query: 512
Effective length of database: 512
Effective search space:   262144
Effective search space used:   262144
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: 53 (25.0 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, or view the source code.

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