GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Shewanella sp. ANA-3

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 7025598 Shewana3_2749 ABC transporter related (RefSeq)

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__ANA3:7025598
          Length = 346

 Score =  103 bits (257), Expect = 4e-27
 Identities = 64/206 (31%), Positives = 117/206 (56%), Gaps = 5/206 (2%)

Query: 21  LQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTPSQGEIIFKGENITGLGSDQIVRR 80
           ++ ++ +I  G +   +GPNG GKST  + + GLL+P+ G+I   GE + G  +++ +RR
Sbjct: 44  VEDLDLAIPKGTIYGFLGPNGCGKSTSIRMLTGLLSPTSGDIRVLGETLPG--AEEKLRR 101

Query: 81  GMCYVPQVCNVFGSLTVAENLDMGAFLHQGPTQTLKDRIYTMFP--KLAQRRNQRAGTLS 138
            + Y+ Q  +++ +L+V ENL+  A ++    +  K R+  +     LA R  Q AG++S
Sbjct: 102 RIGYMTQKFSLYDNLSVRENLEFVAQIYGLNRRQTKARLAELLSLYDLAGREKQMAGSMS 161

Query: 139 GGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFAQIKAINATGKAIILVEQNAKQ 198
           GG++Q LA+  A +  P+LL LDEP++A+ P   ++ + ++  + A G  I++      +
Sbjct: 162 GGQKQRLALAAATLHHPELLFLDEPTSAVDPENRREFWERLFDLCAQGTTILVSTHYMDE 221

Query: 199 ALMMADRGYVLENGRDKLEGSGQSLL 224
           A        +LE G  + +GS Q L+
Sbjct: 222 AERCHGLA-ILERGIKRADGSPQQLM 246


Lambda     K      H
   0.320    0.139    0.393 

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: 165
Number of extensions: 11
Number of successful extensions: 3
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: 240
Length of database: 346
Length adjustment: 26
Effective length of query: 214
Effective length of database: 320
Effective search space:    68480
Effective search space used:    68480
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 (21.8 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