GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braE in Azospirillum thiophilum BV-S

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_045585060.1 AL072_RS29555 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:Q1MCU1
         (463 letters)



>NCBI__GCF_001305595.1:WP_045585060.1
          Length = 497

 Score =  378 bits (971), Expect = e-109
 Identities = 222/452 (49%), Positives = 290/452 (64%), Gaps = 46/452 (10%)

Query: 9   GKPDAGLVRKGLT-EALFAAVLSFGMFVLYVGLKTDQNISNELIIVQRWGLLAIFVAVAA 67
           G+   GL+R+G+    L  AVL  G+ ++   L     +   L++V   G++A+      
Sbjct: 74  GRLGLGLIRQGMALPVLVLAVLCAGIGLV---LPMPTQVLR-LVLVLGGGVIAL------ 123

Query: 68  IGRFAMVVFIRPNIDRRKLSKA-REGELD-ISTEKSFFHRHFLKIALIALLLYPMVVVAI 125
             R AM V       R KLS+A R+  +D ++       R+   +A+   ++ PM  +A 
Sbjct: 124 --RAAMTVAT----GRSKLSQADRDRRMDRVAARVQHASRYIGPVAVAIAVVLPMTPLAD 177

Query: 126 KGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFG 185
           +        + + GI +L Y+ML WGLNIVVGLAGLLDLGYVAFYAVGAYSYALL+ YFG
Sbjct: 178 R-------MLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFG 230

Query: 186 LSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFG 245
           LSFW+ LPL+G+ AA  GV+LGFPVLRLRGDY AIVTL FGEIIR++L+NW   T G  G
Sbjct: 231 LSFWLCLPLAGVLAAFSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILVNWYQFTGGPNG 290

Query: 246 ISSIPKATLFGI------PFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTI 299
           IS IP+ + FGI      P D  A  F ++F L  S  +  +FL+YLILAL ++    T+
Sbjct: 291 ISGIPRPSFFGIAEFSRTPADGMA-AFHEMFGLEFSPLHRIVFLYYLILALALVVNVFTL 349

Query: 300 RLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPE 359
           R+R++P+GRAWEALRED+IAC SLGIN    KL AFA  AMF GFAGSFFA RQGF+SPE
Sbjct: 350 RVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPE 409

Query: 360 SFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRM 419
           SF F+ESA+ILAIVVLGGMGS  G+ +A ++++G  E  RE++              YRM
Sbjct: 410 SFTFIESAIILAIVVLGGMGSQIGVVVATLLVIGLPEAFRELAD-------------YRM 456

Query: 420 LIFGLAMVVVMLFKPRGFVGSREPTAFLRERK 451
           L FG  MVV+ML++PRG +  R+PT  L   K
Sbjct: 457 LAFGAGMVVIMLWRPRGLLAHRDPTILLHGGK 488


Lambda     K      H
   0.330    0.145    0.432 

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: 725
Number of extensions: 43
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: 463
Length of database: 497
Length adjustment: 34
Effective length of query: 429
Effective length of database: 463
Effective search space:   198627
Effective search space used:   198627
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 24 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