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_RS00870 HSERO_RS00870 ABC transporter substrate-binding protein

Query= SwissProt::P21175
         (373 letters)



>FitnessBrowser__HerbieS:HSERO_RS00870
          Length = 378

 Score =  189 bits (479), Expect = 1e-52
 Identities = 114/357 (31%), Positives = 187/357 (52%), Gaps = 8/357 (2%)

Query: 14  AMAIAGFASYSMAADT--IKIALAGPVTGPVAQYGDMQRAGALMAIEQINKAG---GVNG 68
           A ++A   +++MA +T  +KI  + P+TGP A  G   + G +MAIE++N      G   
Sbjct: 12  AASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLNAQPITVGGKK 71

Query: 69  AQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSA 128
            + + +  DD  DPK  VAVA K+ + GVK +VG   S  T PA+ +Y D G+++ T  A
Sbjct: 72  IKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYNDAGIVVATV-A 130

Query: 129 TAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188
           + P+IT +G+  +FR    D+  G     + A+  K K +AV+ D+  YG+G+A E  K 
Sbjct: 131 SNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQGLAQEFIKV 190

Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDAR 248
            +  GI V   +  N    DF A+++ +K      V+ GGY P+ G + RQ KQ G+D  
Sbjct: 191 AKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQMKQLGVDVP 250

Query: 249 FMGPEGVGNSEITAIAGDA-SEGMLATL-PRAFEQDPKNKALIDAFKAKNQDPSGIFVLP 306
            MG +G+ + E+  + GDA  E +  T      ++  + K   D ++ K   P+  + + 
Sbjct: 251 LMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYNRPAETYAVS 310

Query: 307 AYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363
            Y  + +IA+ +++A   DP++   AL   +++   G   FD   DLK    TVY +
Sbjct: 311 FYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSPVTVYRF 367


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: 396
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 373
Length of database: 378
Length adjustment: 30
Effective length of query: 343
Effective length of database: 348
Effective search space:   119364
Effective search space used:   119364
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