GapMind for catabolism of small carbon sources

 

Alignments 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_RS14700 AZOBR_RS14700 C4-dicarboxylate ABC transporter permease

Query= TCDB::Q9RBQ9
         (439 letters)



>FitnessBrowser__azobra:AZOBR_RS14700
          Length = 433

 Score =  236 bits (601), Expect = 1e-66
 Identities = 134/427 (31%), Positives = 238/427 (55%), Gaps = 9/427 (2%)

Query: 15  TVLLFLG--LPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIPLFILMG 72
           T+LL LG  + VA +   +  V   LF      +  +  N   A  S++LT +PLFI MG
Sbjct: 13  TMLLMLGTGIWVALALAGVGFVAMALFTTRPVGM-VMATNIWGASTSWTLTALPLFIWMG 71

Query: 73  ELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLMLPMM 132
           E+LF T ++     G+      LPGRL  + +V  T F+A+SGS+ AT A +G + +P +
Sbjct: 72  EILFRTRISSDMFKGLAPWTGWLPGRLMHVNIVGCTIFAAVSGSSAATAATIGRMTIPEL 131

Query: 133 LARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLAISFV 192
             RGY+P + +G +   G + +LIPPS + ++ G  A +SI++L I GV+PG++L   F+
Sbjct: 132 TRRGYDPMMIVGSLAGAGTLGLLIPPSIIMIVYGVAADVSIARLFIAGVIPGIVLTGLFM 191

Query: 193 AYIVASAKLRPESA-PREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGGVATPTEA 251
            Y+   + L P+   PRE    L   E+ R+    ++P+ L+   ++  I  G+ATPTEA
Sbjct: 192 LYVGGWSLLNPDRVPPREARQSL--MEKIRD-TGSLIPVMLLIAGVLGSIYAGIATPTEA 248

Query: 252 AAIGCAATLAITLMYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFSGATNGI 311
           A IG   +L + L+   + W +   ++ G    S MI FI+  A   +  + ++G    +
Sbjct: 249 AGIGVLGSLLLALVTGTMSWATFRDSVMGAAHTSCMIGFILAGAAFLTVAMGYTGIPRLL 308

Query: 312 VDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQIWFGVMY 371
            + + S  L  A ++ ++    I +G F+D +SM++LT    +P+V++ GID +WFG+  
Sbjct: 309 AEWITSMQLTTASLLVVLTLFFIVMGCFLDGISMVVLTTSVILPMVQNAGIDLLWFGIYI 368

Query: 372 LICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFWPGIATW 431
           +I +++  + PP G  L+ ++ +  K+I    +  +++P+  +   M+ L++ +PG+ +W
Sbjct: 369 IIVVEMAQITPPVGFNLFVLQSMTGKNIF--TIAKASLPFFLMMIVMVALLWIFPGMVSW 426

Query: 432 LPDVFVG 438
           LP + +G
Sbjct: 427 LPSLMIG 433


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: 489
Number of extensions: 25
Number of successful extensions: 3
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: 433
Length adjustment: 32
Effective length of query: 407
Effective length of database: 401
Effective search space:   163207
Effective search space used:   163207
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.

Links

Downloads

Related tools

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