GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__psRCH2:GFF2081
          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:

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