GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natE in Shewanella loihica PV-4

Align NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 5210162 Shew_2606 ABC transporter-related protein (RefSeq)

Query= TCDB::P73650
         (240 letters)



>FitnessBrowser__PV4:5210162
          Length = 272

 Score =  179 bits (453), Expect = 7e-50
 Identities = 104/239 (43%), Positives = 149/239 (62%), Gaps = 8/239 (3%)

Query: 4   LLVVKDVFAGYVADVPILQGINFSIAPGELVTVIGPNGAGKSTLAKTIFGLLTP-----S 58
           LL + ++   Y   + +L+G++  +  GE+VT++GPNGAGKST  K I GLL       S
Sbjct: 13  LLAINNIEVVYDDVIQVLRGVSIEVPQGEIVTLLGPNGAGKSTTLKAISGLLKTENGEVS 72

Query: 59  QGEIIFKGENITGLGSDQIVRRGMCYVPQVCNVFGSLTVAENLDMGAFLHQ-GPTQTLKD 117
           +G+I F GE I    +D +VR G+  V +   +   +TV ENL +GA+  + G      +
Sbjct: 73  RGDIHFMGERIDVKNADDVVRSGLFQVMEGRRIVEDMTVIENLKLGAYTRRDGQVNQDIE 132

Query: 118 RIYTMFPKLAQRRNQRAGTLSGGERQMLAMGRALMLDPDLLLLDEPSAALSPILVKDVFA 177
            ++  FP+L +R    AG LSGGE+QMLA+GRALM  P ++ LDEPS  LSP+LVK+VF 
Sbjct: 133 MVFNYFPRLKERTGL-AGYLSGGEQQMLAIGRALMARPKMICLDEPSMGLSPLLVKEVFG 191

Query: 178 QIKAIN-ATGKAIILVEQNAKQALMMADRGYVLENGRDKLEGSGQSLLNDPLVGELYLG 235
            I+ IN   G  ++LVEQNA  AL  A+ GY++E+G+  L+G+   LLN+  V E YLG
Sbjct: 192 IIEKINREQGITMLLVEQNANYALKAANYGYIMESGKIVLDGTKAQLLNNEDVKEFYLG 250


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: 196
Number of extensions: 7
Number of successful extensions: 4
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: 272
Length adjustment: 24
Effective length of query: 216
Effective length of database: 248
Effective search space:    53568
Effective search space used:    53568
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