GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Shewanella amazonensis SB2B

Align NatE, 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 6939496 Sama_3588 putative ABC-type multidrug transport system, ATPase component (RefSeq)

Query= TCDB::Q8YT15
         (247 letters)



>FitnessBrowser__SB2B:6939496
          Length = 322

 Score = 98.6 bits (244), Expect = 1e-25
 Identities = 70/214 (32%), Positives = 111/214 (51%), Gaps = 8/214 (3%)

Query: 20  GYIKDVDILQGVNFRVESGELVTVIGPNGAGKSTLAKTIFGLLTPHTGKITFKGKNIAGL 79
           G +K VD   GV+  +  G +   +GPNG GKST  + + GLL P +G+I   G+ + G 
Sbjct: 27  GALKAVD---GVDLAIPRGSIYGFLGPNGCGKSTSIRMLTGLLKPTSGEIRVLGEPLKGA 83

Query: 80  KSNQIVRLGMCYVPQIANVFPSLSVEENLEMGAFIRNDSLQPLKDKIFAMFP--RLSDRR 137
           +     R+G  Y+ Q  +++ +L+V ENL   A I        KD+I  +     L  R 
Sbjct: 84  EEKLRRRIG--YMTQKFSLYENLTVLENLRFVARIYGLQGNKAKDRIEQLLSLYSLEGRE 141

Query: 138 RQRAGTLSGGERQMLAMGKALMLEPSLLVLDEPSAALSPILVTQVFEQVKQINQEGTAII 197
            Q AG++SGG++Q LA+  A + EP LL LDEP++A+ P    + +E++  ++ +G   I
Sbjct: 142 SQMAGSMSGGQKQRLALAAATIHEPELLFLDEPTSAVDPENRREFWERLFDLSAKG-CTI 200

Query: 198 LVEQNARKALEMADRGYVLESGRDAISGPGQELL 231
           LV  +     E      +LE G     G  + L+
Sbjct: 201 LVSTHYMDEAERCHGLAILERGIKRADGSPKALM 234


Lambda     K      H
   0.317    0.136    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: 173
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: 247
Length of database: 322
Length adjustment: 26
Effective length of query: 221
Effective length of database: 296
Effective search space:    65416
Effective search space used:    65416
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: 47 (22.7 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