GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Herbaspirillum seropedicae SmR1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__HerbieS:HSERO_RS08920
          Length = 655

 Score =  244 bits (622), Expect = 4e-69
 Identities = 124/250 (49%), Positives = 170/250 (68%)

Query: 9   VLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFEL 68
           +LKV  I  +FGGL+AL+ V + +++G V+GLIGPNG+GK+T  NV+TG+Y P  G  E 
Sbjct: 392 LLKVNQILMQFGGLKALNRVDLDVRKGTVHGLIGPNGSGKSTMMNVLTGIYRPTDGVVEY 451

Query: 69  AGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFK 128
            G+P        +A  G+ARTFQN++LF EMTA ENV+VG H    S +   +  T  + 
Sbjct: 452 DGRPISGNVPSAIALGGVARTFQNVQLFGEMTATENVLVGLHHTFNSNVVDVMANTPRYV 511

Query: 129 AEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGM 188
            EE A  +RA  +L++VG+   A+ +AR L YG QR LEI RAL  +P L+ LDEPAAG+
Sbjct: 512 REEQAARERAAAILEFVGLANLANEEARNLPYGKQRLLEIGRALGLNPSLLLLDEPAAGL 571

Query: 189 NATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQKNE 248
            A +  +L  +I +IR    TI+LIEH + +VM +CD VTVLD+G++IAEG PA+VQ + 
Sbjct: 572 TAPDIKELVAIIRKIREAGITIILIEHHMDVVMSICDTVTVLDFGQKIAEGKPAQVQADP 631

Query: 249 KVIEAYLGTG 258
           KVIEAYLG+G
Sbjct: 632 KVIEAYLGSG 641


Lambda     K      H
   0.319    0.137    0.384 

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: 441
Number of extensions: 20
Number of successful extensions: 2
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: 260
Length of database: 655
Length adjustment: 31
Effective length of query: 229
Effective length of database: 624
Effective search space:   142896
Effective search space used:   142896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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