GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Herbaspirillum seropedicae SmR1

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate HSERO_RS08920 HSERO_RS08920 ABC transporter

Query= TCDB::Q7A2H0
         (260 letters)



>FitnessBrowser__HerbieS:HSERO_RS08920
          Length = 655

 Score =  198 bits (504), Expect = 2e-55
 Identities = 107/249 (42%), Positives = 156/249 (62%), Gaps = 1/249 (0%)

Query: 11  LLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVIF 70
           LL  + +   FGG+KA+    ++V +G++ GLIGPNG+GK+T+ N+L+   RP  G V +
Sbjct: 392 LLKVNQILMQFGGLKALNRVDLDVRKGTVHGLIGPNGSGKSTMMNVLTGIYRPTDGVVEY 451

Query: 71  DGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVVV 130
           DG PI    P  IA  G+ RTFQ  +    ++  EN+L+        N   V       V
Sbjct: 452 DGRPISGNVPSAIALGGVARTFQNVQLFGEMTATENVLVGLHHTFNSNVVDVMANTPRYV 511

Query: 131 KEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAGV 190
           +EE+  +E+A  +LE VGLA  A E A  L  G+++LLE+GRAL  NP L+LLDEPAAG+
Sbjct: 512 REEQAARERAAAILEFVGLANLANEEARNLPYGKQRLLEIGRALGLNPSLLLLDEPAAGL 571

Query: 191 NPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQTN 250
               I ++   I+   R+ G+T ++IEH+MDV+MS+CD V VL  GQ +A+G PA++Q +
Sbjct: 572 TAPDIKELV-AIIRKIREAGITIILIEHHMDVVMSICDTVTVLDFGQKIAEGKPAQVQAD 630

Query: 251 SQVLEAYLG 259
            +V+EAYLG
Sbjct: 631 PKVIEAYLG 639


Lambda     K      H
   0.319    0.136    0.391 

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: 350
Number of extensions: 11
Number of successful extensions: 2
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: 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