GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braC in Herbaspirillum seropedicae SmR1

Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate HSERO_RS17350 HSERO_RS17350 ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__HerbieS:HSERO_RS17350
          Length = 380

 Score =  221 bits (563), Expect = 3e-62
 Identities = 136/367 (37%), Positives = 197/367 (53%), Gaps = 9/367 (2%)

Query: 11  LFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG---GVN 67
           L AA+ +A FA  + + + +KIA  GP++GP A  G     GA MA++++N  G   G  
Sbjct: 10  LTAAIGLA-FAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNAKGFTIGGK 68

Query: 68  GAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPS 127
             + E V  DDA DPKQA AVA K+V+  V  V+GH+ S +T PA+ IY D G+  ++PS
Sbjct: 69  KVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDAGIPQVSPS 128

Query: 128 ATAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKK 187
           AT P+ T +G+K  FR +  D   G   GK+  ++   K IAV+ D+  YG+G+A E  K
Sbjct: 129 ATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQGVADEFAK 188

Query: 188 TVEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDA 247
             + AG  +   +  N    DFNA+++ LK      V+FGG     G +LRQ KQ G+ A
Sbjct: 189 GAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQMKQLGISA 248

Query: 248 RFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQDPSGIFVL-- 305
           +FMG +G+    +  +AGD           A   D   K  +D F+A  +   GI V+  
Sbjct: 249 KFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKKKFGIDVVYN 308

Query: 306 --PAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363
              AY A   +A  + KAG ADP+K    L   + +  TG + FD KGD+K+   T+Y  
Sbjct: 309 AAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIKDGSLTLYT- 367

Query: 364 HKDATRT 370
           +K   RT
Sbjct: 368 YKGGQRT 374


Lambda     K      H
   0.316    0.133    0.377 

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: 389
Number of extensions: 28
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: 373
Length of database: 380
Length adjustment: 30
Effective length of query: 343
Effective length of database: 350
Effective search space:   120050
Effective search space used:   120050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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