GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fcbT3 in Azospirillum brasilense Sp245

Align FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate AZOBR_RS20015 AZOBR_RS20015 C4-dicarboxylate ABC transporter

Query= TCDB::Q9RBQ9
         (439 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS20015 AZOBR_RS20015
           C4-dicarboxylate ABC transporter
          Length = 503

 Score =  214 bits (544), Expect = 7e-60
 Identities = 132/438 (30%), Positives = 219/438 (50%), Gaps = 21/438 (4%)

Query: 9   LLLGGTTVLLFLGLPVAYSFFA----INVVGAWLFLGGDSALGQLVRNGLVAVASFSLTP 64
           L+     + L +G PVA++  A      ++G  L L   +    L       + + +L  
Sbjct: 12  LMFAALVLFLLMGFPVAFALAANGLLFGLIGIELGLLTPALFQALPERVFGIMRNDTLLA 71

Query: 65  IPLFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAML 124
           IP F  MG +L  +G+A+  +D + ++   L G LA   +  G   +A +G   A+   +
Sbjct: 72  IPFFTFMGLILERSGMAEDLLDTVGQLFGPLRGGLAYAVIFVGALLAATTGVVAASVISM 131

Query: 125 GSLMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPG 184
           G + LP+ML  GY+ +L  G I A G +  +IPPS + ++L    G S+  +  G ++PG
Sbjct: 132 GLISLPIMLRYGYDRRLASGVIAASGTLAQIIPPSLVLIILADQLGRSVGDMYAGALVPG 191

Query: 185 LLLAISFVAYIVASAKLRPESAPR--EELVVLRGWE-RWRELVVYVLPLSLIFVAIVAVI 241
           L+L   +  YI+  + +RPE  P    E   LRG++  +R L   V PL LIF+ ++  I
Sbjct: 192 LVLTGLYAGYILVVSIVRPEFTPALPPEARSLRGFQLLFRVLTSLVPPLVLIFL-VLGTI 250

Query: 242 SGGVATPTEAAAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQV 301
             G+ATPTE  A+G A  + + LM R L W  + QA+  T  +S  ++FI++ +T F  V
Sbjct: 251 FIGIATPTEGGAMGAAGAMILALMKRQLSWSLMRQAMDTTAKLSSFVIFILIGSTVFGLV 310

Query: 302 LSFSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLG 361
                    +  L+ S      G + ++  ++  L  F+D   +  + +P   P+ + LG
Sbjct: 311 FRAVNGDLWVEHLLTSLPGGELGFLIVVNIMVFLLAFFLDFFELAFIIVPLLAPVAEKLG 370

Query: 362 IDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAP-------------KHITMGQVFASA 408
           ID IWFGV+  + MQ   + PP G  L+ ++ VAP             K IT GQ++  A
Sbjct: 371 IDLIWFGVLLGVNMQTSFMHPPFGFALFFLRSVAPREDYKDKITGKIIKKITTGQIYWGA 430

Query: 409 MPYVGLSFTMLILIFFWP 426
           +P+V +   M+ L+  +P
Sbjct: 431 VPFVCIQLIMVALVIMFP 448


Lambda     K      H
   0.329    0.143    0.433 

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: 586
Number of extensions: 45
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: 439
Length of database: 503
Length adjustment: 33
Effective length of query: 406
Effective length of database: 470
Effective search space:   190820
Effective search space used:   190820
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