Alignments for a candidate for mctP in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mctP in Paraburkholderia bryophila 376MFSha3.1

Align Na+/solute symporter (characterized, see rationale)
to candidate H281DRAFT_03156 H281DRAFT_03156 solute:Na+ symporter, SSS family

Query= uniprot:B2T7V3
         (493 letters)



>FitnessBrowser__Burk376:H281DRAFT_03156
          Length = 493

 Score =  927 bits (2396), Expect = 0.0
 Identities = 469/493 (95%), Positives = 480/493 (97%)

Query: 1   MSDVNPVNPVAMTVFIAFFVLVTVIGFFAARWKRGDLTQLHEWGLGGRQFGTVISWFLVG 60
           M+D+NPVNPVAMTVFIAFFVLVTVIGFFAARWKRGDLTQLHEWGLGGRQFGTVISWFLVG
Sbjct: 1   MNDLNPVNPVAMTVFIAFFVLVTVIGFFAARWKRGDLTQLHEWGLGGRQFGTVISWFLVG 60

Query: 61  GDFYTAYTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWKIAHAKNHITAADYV 120
           GDFYTAYTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWK+AHAKNHITAADYV
Sbjct: 61  GDFYTAYTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWKVAHAKNHITAADYV 120

Query: 121 QGEYGGKWFPAAVAITGIVATMPYIALQLVGMQVVIKGLGVTGEMPLIVAFVILALYTYA 180
            GEYGGKWFPAAVA+TGIVATMPYIALQLVGMQVVIKGLGVTGE+PLIVAFVILALYTYA
Sbjct: 121 HGEYGGKWFPAAVALTGIVATMPYIALQLVGMQVVIKGLGVTGELPLIVAFVILALYTYA 180

Query: 181 SGLRAPAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVFDAADTYFKAKGGATGIILKPT 240
           SGLRAPAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVFDAADTYFKAKGGATGIILKPT
Sbjct: 181 SGLRAPAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVFDAADTYFKAKGGATGIILKPT 240

Query: 241 QFTAYASLALGSALAAFMYPHTMTAVLSSSSANTVRKNAIFLPAYTLLLGLIALLGYMAI 300
           QFTAYASLALGSALAAFMYPHTMTAVLSSSSA TVRKNAIFLPAYTLLLGLIALLGYMAI
Sbjct: 241 QFTAYASLALGSALAAFMYPHTMTAVLSSSSATTVRKNAIFLPAYTLLLGLIALLGYMAI 300

Query: 301 AAGVHVKSASDMVPALFNTLFPSWFVGFAAAAIAISALVPAAIMSIGAANLFTRNLWRPL 360
           AAGVHVKSASD+VP LF TLFPSWFVGFAAAAIAISALVPAAIMSIGAANLFTRNLWRPL
Sbjct: 301 AAGVHVKSASDIVPTLFGTLFPSWFVGFAAAAIAISALVPAAIMSIGAANLFTRNLWRPL 360

Query: 361 VSPNISPEGEASTAKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWILQIFPAIVFSLY 420
           VSPNI+PE EAS AKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWILQIFPAIVFSLY
Sbjct: 361 VSPNITPEAEASNAKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWILQIFPAIVFSLY 420

Query: 421 TRRLNTPGLFLGWLAGIVLGTGLAISQGLKPVFALHLGDAVYPVYIGLIALTVNIVVSFV 480
           TRRLNTPGLF GWL GIVLGT LAISQGLKPVFALHLGDAVYP+YIGLIAL VNIVV+FV
Sbjct: 421 TRRLNTPGLFAGWLVGIVLGTALAISQGLKPVFALHLGDAVYPIYIGLIALVVNIVVTFV 480

Query: 481 VSVLSPRRVVAAA 493
           VS +SPRRV  +A
Sbjct: 481 VSAVSPRRVAVSA 493


Lambda     K      H
   0.328    0.141    0.431 

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: 1029
Number of extensions: 42
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: 493
Length of database: 493
Length adjustment: 34
Effective length of query: 459
Effective length of database: 459
Effective search space:   210681
Effective search space used:   210681
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 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