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 TRAP transporter, subunit DctM (characterized, see rationale)
to candidate GFF1297 PGA1_c13130 TRAP transporter, subunit DctM

Query= uniprot:I7DRS6
         (467 letters)



>FitnessBrowser__Phaeo:GFF1297
          Length = 491

 Score =  243 bits (621), Expect = 8e-69
 Identities = 154/518 (29%), Positives = 249/518 (48%), Gaps = 99/518 (19%)

Query: 3   VVLLFSMVIGLLLIGVPIAVAL-GLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIP 61
           ++    + + LLLIG+P+   L      L  L   +  L  +   L+   +  F L+AIP
Sbjct: 2   LIWFLPLFLFLLLIGLPVFFCLLAAPGALLWLNGQERDLTLLYRNLYNGMDS-FPLMAIP 60

Query: 62  FFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGS 121
           FF+LA   M  GG+  R++ FS A +GHL GGLA   + + +LFA LSGS+ A   A+GS
Sbjct: 61  FFMLAGELMNRGGITVRLVEFSQALMGHLRGGLAQVNILSSILFAGLSGSAVADTSALGS 120

Query: 122 IVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLM 181
           ++I  M + GYS++FAA V   +  +G +IPPS +M++YA  +  SV  +FLAG++PG++
Sbjct: 121 MLIPAMEREGYSRKFAAAVTAASSVIGPIIPPSGIMIIYAYVMGESVAALFLAGIVPGVL 180

Query: 182 AGLMLMVTIYVMAKVKNLPKG--------------EWLGWGEV--------------AAS 213
            G+ LM+ +  MA    LP                 W  +G V              A  
Sbjct: 181 VGVGLMIMVRAMADRYELPAARRVVFDSVEIGVMERWFSFGLVRLNLGLLLAQFVPLAEG 240

Query: 214 AANASVGLLLIGIIL-----------------------------------GGIYGGIFTP 238
           A      L   G +L                                   GGI  G+FTP
Sbjct: 241 AGAQMKWLAFFGAVLFAHGLMLGLRRVVSPAFRTICKRAVVPLQTPVLILGGILAGVFTP 300

Query: 239 TEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHAD 298
           TEAAAVA  YA  ++  V   +G ++ A  P+                            
Sbjct: 301 TEAAAVAVAYALLISFLV---LGSMRLADLPQ---------------------------- 329

Query: 299 TRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVIL 358
                  AG  +  +L ++  A+  K V++    P+Q+A  +L+    P++ L ++N++L
Sbjct: 330 ---VFSRAGITSAVVLLLVGAAMSFKTVVSLSHAPEQLADFILTLSENPLILLFLINLLL 386

Query: 359 LIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSG 418
            + G F++    ++I+ P++ P+  +LG++ +H  IIM VN+ +G+ TPP+GL LFV + 
Sbjct: 387 FVVGMFLDAGPAIIILGPILGPVFTDLGVESVHFAIIMCVNLTVGLATPPMGLVLFVAAA 446

Query: 419 VAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456
           V+   +  + +A LPFLA+    + +IT++P IS  +P
Sbjct: 447 VSQERVTTIAKAILPFLAIEIAVIFLITFVPAISLTIP 484



 Score = 25.8 bits (55), Expect = 0.003
 Identities = 40/201 (19%), Positives = 81/201 (40%), Gaps = 11/201 (5%)

Query: 9   MVIGLLLIGV-----PIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFF 63
           +++G +L GV       AVA+  +  +  L+     LA +      A  G  + + +   
Sbjct: 288 LILGGILAGVFTPTEAAAVAVAYALLISFLVLGSMRLADLPQVFSRA--GITSAVVLLLV 345

Query: 64  ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAA--LSGSSPATVVAIGS 121
             A SF T   ++    + +   +      L +  +   +LF       + PA ++ +G 
Sbjct: 346 GAAMSFKTVVSLSHAPEQLADFILTLSENPLILLFLINLLLFVVGMFLDAGPAIII-LGP 404

Query: 122 IVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLM 181
           I+      +G      A ++C   T+G+  PP  +++  AAAV           ++P L 
Sbjct: 405 ILGPVFTDLGVESVHFAIIMCVNLTVGLATPPMGLVLFVAAAVSQERVTTIAKAILPFLA 464

Query: 182 AGLMLMVTI-YVMAKVKNLPK 201
             + ++  I +V A    +P+
Sbjct: 465 IEIAVIFLITFVPAISLTIPR 485


Lambda     K      H
   0.329    0.144    0.421 

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: 692
Number of extensions: 37
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 467
Length of database: 491
Length adjustment: 34
Effective length of query: 433
Effective length of database: 457
Effective search space:   197881
Effective search space used:   197881
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 Sep 17 2021. 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