GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fcbT3 in Pseudomonas stutzeri RCH2

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 GFF360 Psest_0361 TRAP transporter, DctM subunit

Query= TCDB::Q9RBQ9
         (439 letters)



>FitnessBrowser__psRCH2:GFF360
          Length = 426

 Score =  197 bits (501), Expect = 5e-55
 Identities = 130/432 (30%), Positives = 225/432 (52%), Gaps = 13/432 (3%)

Query: 7   AWLLLGGTTVLLFLGLPVAYSFFAINVVGAWLFLGGDSALGQLVRNGLVAVASFSLTPIP 66
           A +LLG   VL+ L +PVAYS     +VGAW     D  L  ++      V  FSL  IP
Sbjct: 3   AVVLLGSFIVLILLRVPVAYSLGLATLVGAWWI---DIPLHAVMIQIAGGVNKFSLLAIP 59

Query: 67  LFILMGELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGS 126
            F+L G ++   G+A+R +     ++  + G L+++ + A TFF AISGS++A TA +GS
Sbjct: 60  FFVLAGAIMAEGGMARRLVAFAGVLVGFVRGGLSLVNITASTFFGAISGSSLADTASVGS 119

Query: 127 LMLPMMLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAG--ISISKLLIGGVLPG 184
           +++P M  +GY  +      I+     +L PPS  +V+    AG  +SI+ L + G+ PG
Sbjct: 120 VLIPEMEKKGYPREFSTAVTISGSVQALLTPPSHNSVIYSLAAGGTVSIAALFVAGIGPG 179

Query: 185 LLLAISFVAYIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGG 244
           LLL+ +     +  A+ R  + P+ E+V LR   +  ++ V  L   +  V I+  I  G
Sbjct: 180 LLLSATMATLCLLFARKR--NYPKGEVVPLR---QALKICVEALWGLMTMVIILGGILSG 234

Query: 245 VATPTEAAAIGCAATLAITL-MYRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLS 303
           V T TE+AA+       +T+ +YR  +W  L + L  TV    +++ +I  A +F  +++
Sbjct: 235 VFTATESAAVAVVWAFFVTMFIYRDYKWSELPRMLHRTVRTLSIVMILIAFAASFGYIMT 294

Query: 304 FSGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGID 363
                + I     +       ++  +  +L+ LG  +D   ++L+  P  +P+V S G+D
Sbjct: 295 LMQIPSKITTAFLALSDNRYVILMCINFMLLVLGTLMDMAPLILILTPILLPVVVSFGVD 354

Query: 364 QIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIF 423
            + FG++ L+ + +GL+ PP G +L+   G A   +T+     + +P+    F +L+ + 
Sbjct: 355 PVHFGMIMLVNLGIGLITPPVGAVLFV--GAAIGKVTIENTVKALLPFYAALFAVLMAVT 412

Query: 424 FWPGIATWLPDV 435
           + P I+ WLP V
Sbjct: 413 YIPMISLWLPSV 424


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: 437
Number of extensions: 23
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: 426
Length adjustment: 32
Effective length of query: 407
Effective length of database: 394
Effective search space:   160358
Effective search space used:   160358
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