Alignments for a candidate for dctM in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for dctM in Phaeobacter inhibens BS107

Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate GFF1982 PGA1_c20160 TRAP transporter, subunit DctM

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__Phaeo:GFF1982
          Length = 785

 Score =  156 bits (394), Expect = 3e-42
 Identities = 129/381 (33%), Positives = 184/381 (48%), Gaps = 53/381 (13%)

Query: 90  LLETMGILLGRLRG------GLALAVVLVGALLAATTGVVAATV-----VAMGLISLPIM 138
           L+  MG++L   RG         L +  +G LL A   VVA        + + LI+LP +
Sbjct: 428 LMVLMGLVLAVGRGVSPSSDPKPLILGAIGVLLIALVDVVAIAPTTSPGITVLLIALPTL 487

Query: 139 LRYGYNKELATGVIAASGTLGQIIPPSVVLV-VLGDQLGISVGDLFIGSVIPGLMMASAF 197
           L   Y   +A G  A +  +  + PP +++V VLG  LG        G   P    A   
Sbjct: 488 LAL-YGCRIAAGRSARNDLIRVVFPPLILIVAVLGSILG--------GITNPTPAAALGA 538

Query: 198 ALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIFFGFATPT 257
              +++ A+ +            +  GK+ GK +I       I IL+    + F      
Sbjct: 539 GGAIMLAAYRK-----------LQDQGKS-GKIIIWATFAVAICILV---GVNFDLRING 583

Query: 258 EAGAVGCAGAIALAAANGQFTLES---------------LRQVCDTTLRITSMVVFILIG 302
            +G V     IA   A G +                   L  V   T ++TSMV  ILIG
Sbjct: 584 RSG-VSAETVIAFGVAYGAYLFALFGLLYGCWVLFKGGVLTPVVRETAKVTSMVFTILIG 642

Query: 303 STAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFV 362
           S   +LV     G+ ++   L +       FL V M  +F+LGF +DF EI +IVIP+  
Sbjct: 643 SQLLNLVVISFGGEHYIQQFLKSFDSELKVFLIV-MVVLFILGFVLDFLEIIYIVIPIVG 701

Query: 363 PVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILL 422
           PV      D  W  +++  NLQTSFLTPPFGFALFYLRGVAP EVTT+ IYRGV+PF+L+
Sbjct: 702 PVIYGGSFDPKWVTIMVAVNLQTSFLTPPFGFALFYLRGVAPKEVTTAHIYRGVLPFVLI 761

Query: 423 QLLVLLLIIIFPGIVSFLPSL 443
           Q++ L ++ +FP IV+ +P+L
Sbjct: 762 QVVGLGILWMFPSIVTIVPAL 782



 Score =  153 bits (387), Expect = 2e-41
 Identities = 88/189 (46%), Positives = 118/189 (62%), Gaps = 28/189 (14%)

Query: 55  MPQRIFGIMANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGA 114
           M +R+    +  TLLA+  F+ MG  LE+S IA  LL TM  + G L GGLA+++V+VGA
Sbjct: 113 MNERVLAGASIETLLAVLMFVLMGITLERSKIANDLLTTMARVFGPLPGGLAVSIVVVGA 172

Query: 115 LLAATTGVVAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQ 174
            LAA+TG+V ATVV MGL++LP MLR  Y+ ELATGVIAASGTLGQIIPPS+V+V+LG  
Sbjct: 173 FLAASTGIVGATVVTMGLLALPTMLRNNYSPELATGVIAASGTLGQIIPPSIVIVLLGTL 232

Query: 175 LG----------------------------ISVGDLFIGSVIPGLMMASAFALHVLIVAF 206
            G                            +SVG LF  +++PG+M+A  +AL+    A 
Sbjct: 233 AGDLYSTAQEARAQEFGCSDALTYLGEPAVVSVGTLFQAALLPGIMLALLYALYAFGYAL 292

Query: 207 IRPDVAPAL 215
           + P+ APA+
Sbjct: 293 LNPEKAPAV 301


Lambda     K      H
   0.331    0.149    0.437 

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: 820
Number of extensions: 41
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 445
Length of database: 785
Length adjustment: 37
Effective length of query: 408
Effective length of database: 748
Effective search space:   305184
Effective search space used:   305184
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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