Alignments for a candidate for dctM in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for dctM in Cereibacter sphaeroides ATCC 17029

Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_002720648.1 RSPH17029_RS10760 TRAP transporter large permease

Query= uniprot:Q88NP0
         (426 letters)



>NCBI__GCF_000015985.1:WP_002720648.1
          Length = 426

 Score =  422 bits (1085), Expect = e-122
 Identities = 208/423 (49%), Positives = 301/423 (71%)

Query: 1   MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60
           ME FIL GSF+ L+LIG PVA+ LG+S+ +   ++ +P   +  ++ SGV+ ++L+AIPF
Sbjct: 1   MELFILFGSFVFLLLIGTPVAFCLGVSSFLTVLYLGLPPVVVFQRLNSGVSVYALMAIPF 60

Query: 61  FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120
           F+ +G +M  G ++RRLVA AG LVG +RGGL  VN++AS  FG +SGS+ AD ++VG +
Sbjct: 61  FIYSGDLMVRGDIARRLVALAGALVGHLRGGLGQVNVVASVMFGGVSGSAAADASAVGGL 120

Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL 180
           ++P+M+ +GY  +++  +TV GS+ AL+ PPSHN ++YS+AAGG +SIA LF AGI+PGL
Sbjct: 121 MVPQMKARGYGVDYAVNLTVVGSIIALMIPPSHNMIIYSIAAGGRISIADLFTAGIIPGL 180

Query: 181 LLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATE 240
           LL+  +M      A++R YP      LR    I   A+ GL+ + +I GG+ SG+FTA+E
Sbjct: 181 LLALGLMVAAYFVARRRGYPTERFPGLRALGAIFVSAVPGLILVALIFGGVRSGIFTASE 240

Query: 241 SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPS 300
           SA +AVV++  VT+ IYR   W +        VRT ++V+++IG AASFG+++  +++P+
Sbjct: 241 SANIAVVYALLVTILIYRTLTWSEFVHATIGAVRTTAMVLLVIGCAASFGWLLAYLKVPT 300

Query: 301 KITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGM 360
            +      LSDN  VIL+ IN  L++LGT MDM+PLI+I TPI LPV    GVDPVHFG+
Sbjct: 301 ALVAFMQGLSDNPLVILLLINVALLVLGTFMDMSPLIVITTPIFLPVAQAFGVDPVHFGV 360

Query: 361 IMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW 420
           I+++NLGIGL TPPVGAVLFVG A+G++SI + ++ + PFY A   VL+ VTYIPA+SLW
Sbjct: 361 ILILNLGIGLCTPPVGAVLFVGCAVGRISIWTAMRTIWPFYGAALAVLLLVTYIPALSLW 420

Query: 421 LPS 423
           LP+
Sbjct: 421 LPA 423


Lambda     K      H
   0.329    0.142    0.418 

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: 573
Number of extensions: 25
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: 426
Length of database: 426
Length adjustment: 32
Effective length of query: 394
Effective length of database: 394
Effective search space:   155236
Effective search space used:   155236
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: 51 (24.3 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Sep 17 2021.

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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