GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Herbaspirillum seropedicae SmR1

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__HerbieS:HSERO_RS08920
          Length = 655

 Score =  201 bits (511), Expect = 3e-56
 Identities = 107/250 (42%), Positives = 158/250 (63%)

Query: 16  SSLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEV 75
           ++LL    +   FGGL+A++  D+ V++G++ GLIGPNG+GK+T+ N+L+   RP  G V
Sbjct: 390 ATLLKVNQILMQFGGLKALNRVDLDVRKGTVHGLIGPNGSGKSTMMNVLTGIYRPTDGVV 449

Query: 76  LFNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRR 135
            ++G  I    P  IAL G  RTFQ  ++   +T  EN+L+   H      +  + N  R
Sbjct: 450 EYDGRPISGNVPSAIALGGVARTFQNVQLFGEMTATENVLVGLHHTFNSNVVDVMANTPR 509

Query: 136 VQKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAA 195
             +EE+A RE+A A+LE VGL   A + A  L  G+++LLE+ RAL  NP L+LLDEPAA
Sbjct: 510 YVREEQAARERAAAILEFVGLANLANEEARNLPYGKQRLLEIGRALGLNPSLLLLDEPAA 569

Query: 196 GVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255
           G+    I ++   I      GIT ++IEH+MDV+M++C  V VL  G+ +A+G P Q+Q+
Sbjct: 570 GLTAPDIKELVAIIRKIREAGITIILIEHHMDVVMSICDTVTVLDFGQKIAEGKPAQVQA 629

Query: 256 DPRVLEAYLG 265
           DP+V+EAYLG
Sbjct: 630 DPKVIEAYLG 639


Lambda     K      H
   0.319    0.136    0.389 

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: 407
Number of extensions: 14
Number of successful extensions: 1
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: 267
Length of database: 655
Length adjustment: 31
Effective length of query: 236
Effective length of database: 624
Effective search space:   147264
Effective search space used:   147264
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