GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsB in Halopiger salifodinae KCY07-B2

Align ABC transporter permease (characterized, see rationale)
to candidate WP_049992209.1 LT39_RS19805 sugar ABC transporter permease

Query= uniprot:A0A165KPZ4
         (293 letters)



>NCBI__GCF_000784335.1:WP_049992209.1
          Length = 317

 Score =  151 bits (382), Expect = 2e-41
 Identities = 97/270 (35%), Positives = 146/270 (54%), Gaps = 7/270 (2%)

Query: 17  PAFVLGFAFIYGLMVWNGVLSLTVSRML--PNYEWAGLAQYERLWEMDRWWVALKNLGIF 74
           P  ++G A +YG + +N  +S T    +  P +    L  Y      + +  A  N  + 
Sbjct: 42  PFILMGIA-VYGGIGYNIAISFTDYAGIGQPTFSSFDLEMYREALASEAFREAAFNNFVL 100

Query: 75  GVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLNPGLGI-E 133
            + +   SL +G+ LA+LLD  IR +  ++TIYL PMALSFVVT   W W+ NP  G+  
Sbjct: 101 LIAFTTISLALGLFLAILLDHGIRYKDKIQTIYLLPMALSFVVTAQLWLWMFNPESGVLT 160

Query: 134 KMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIKAAQVD 193
            +V   GF   +  WL +  +A+  V+ A +WQ +G+AM ++LAGL+ I     +AA VD
Sbjct: 161 VIVTTLGFEPID--WLGNPRLALPAVIFALVWQFSGYAMVVYLAGLQSIPADQFEAANVD 218

Query: 194 GASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAG-GPGFATDVPATFMYT 252
           GAS  R Y RI++P L+    S  +VL   A+K+F  + +L     P   TD+ AT M  
Sbjct: 219 GASTIRTYLRIIVPQLKESSVSAAVVLMVFALKAFTFLYSLVGQYRPPNGTDILATLMVR 278

Query: 253 MSFSRGQIGLGAASATMMLATVAALVIPYL 282
            +F  G+   GAA ATM+L    +++ PYL
Sbjct: 279 QAFKFGKWAYGAAIATMLLLLALSVIAPYL 308


Lambda     K      H
   0.327    0.141    0.451 

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: 268
Number of extensions: 16
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: 293
Length of database: 317
Length adjustment: 27
Effective length of query: 266
Effective length of database: 290
Effective search space:    77140
Effective search space used:    77140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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