GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctM in Pseudomonas stutzeri RCH2

Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate GFF2081 Psest_2124 TRAP transporter, DctM subunit

Query= reanno::PV4:5208943
         (465 letters)



>lcl|FitnessBrowser__psRCH2:GFF2081 Psest_2124 TRAP transporter,
           DctM subunit
          Length = 425

 Score =  228 bits (581), Expect = 3e-64
 Identities = 141/453 (31%), Positives = 240/453 (52%), Gaps = 39/453 (8%)

Query: 1   MTIATLFISLFLCMLLGMPIAIALGF--SSMLTILLFSDDSLASVALKLYESTSEHYTLL 58
           MT+     SL   M LGMPIA AL    S ++  L F D  L +  L   ++ ++ + LL
Sbjct: 1   MTVVVFLSSLLGFMTLGMPIAFALLLTGSVLMWYLDFWDVQLLAQNL---QAGADSFPLL 57

Query: 59  AIPFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAA 118
           A+PFFIL+   ++ GG++RRII  A    GH RGGL   ++ A +L A++SGS+ A  AA
Sbjct: 58  AVPFFILAGELMNAGGISRRIIAMAQAYFGHKRGGLGYVAIAASVLLASMSGSALADTAA 117

Query: 119 IGSIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIP 178
           + ++++  M   GYP   ++G++   G +  +IPPS+  ++Y   T  S +++F+AG++P
Sbjct: 118 LATLLLPMMRERGYPLSSSSGLVAAGGIIAPIIPPSMPFVIYGVVTGTSISQLFLAGMVP 177

Query: 179 GLMMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASP 238
           GL+MG+ L++A  ++AR    P +                  L L VI++G + GG+ +P
Sbjct: 178 GLIMGMGLIVAWTLIARRIDEPKQEKASAAERRRVLVDGAAALMLPVIIVGGLRGGLFTP 237

Query: 239 TEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKE 298
           TEAA VA VYA  ++   YR++      +W    E L RA                    
Sbjct: 238 TEAAVVAAVYALAVSTLLYREL------NWAGLVEVLTRA-------------------- 271

Query: 299 IRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLL 358
                   ++ +  ++F+ A A + A+++T  ++P  IA  +  +       ++ + LL+
Sbjct: 272 --------SRTTASVMFLCAAATVSAYMITLAQLPDEIAAMLGPLAQDPKLLMVAIMLLM 323

Query: 359 LAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAG 418
           +A G  ++ +  +LI+ P+L PIA + GIDP++ G++ V+   IG++TPPVG  L V  G
Sbjct: 324 IAVGMVLDLTPTILILGPVLAPIAIKAGIDPVYFGVMFVLIGSIGLITPPVGTVLNVVGG 383

Query: 419 ITGRSMGWVIHSCIPWLALLLFFLALITYIPQI 451
           I    M  ++   +P+  + L  + L+  +P I
Sbjct: 384 IGRLRMETLVRGVMPFFLIYLVIVGLLIAVPSI 416


Lambda     K      H
   0.330    0.144    0.424 

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: 553
Number of extensions: 36
Number of successful extensions: 5
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: 465
Length of database: 425
Length adjustment: 32
Effective length of query: 433
Effective length of database: 393
Effective search space:   170169
Effective search space used:   170169
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:

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:

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:

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