GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2561 in Mesorhizobium ciceri WSM1271

Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate YP_004141854.1 Mesci_2669 binding-protein-dependent transport system inner membrane protein

Query= reanno::acidovorax_3H11:Ac3H11_2561
         (252 letters)



>NCBI__GCF_000185905.1:YP_004141854.1
          Length = 282

 Score =  193 bits (490), Expect = 4e-54
 Identities = 99/245 (40%), Positives = 156/245 (63%), Gaps = 1/245 (0%)

Query: 3   ARARWM-LGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKEGWLLFTEYGFIKDIGMT 61
           AR+R++ + +A FV     W   T  G V P FL SP ++A +   L  +     D+  +
Sbjct: 31  ARSRFLVIAVAVFVGLGLAWWAATGLGLVKPIFLPSPGSVAMQIAKLAADGTLWLDLKAS 90

Query: 62  IWRVVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPASAFIPLLILWAGIGEA 121
           ++R+  GF++A+ +++P+G+ +G+++  EA  EP + F RY+P  AF+PL ILWAG G++
Sbjct: 91  MYRISIGFLIASALSIPIGVLIGSFRSWEAAIEPLVDFIRYMPVVAFVPLSILWAGTGDS 150

Query: 122 QKILVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVTRVLIPGAAPEIAETL 181
           QK L+IFIG+ FQ  LM+   V     D +    TLG   + I+TR+++P A P I +TL
Sbjct: 151 QKFLIIFIGTFFQQVLMIMDNVKRVPADFIGLGRTLGLPDRKILTRIVVPSALPGIWDTL 210

Query: 182 RLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIIIIGLIGLVSDFAFKAL 241
           R+ LGWAWT++++AEL+ ++SG+G+ IT SQ    T  II  I+++GL+GL++D   KAL
Sbjct: 211 RISLGWAWTWLVLAELVAATSGLGYRITVSQRYFQTNTIIGYILLLGLLGLITDQVMKAL 270

Query: 242 NHRLF 246
              LF
Sbjct: 271 EKVLF 275


Lambda     K      H
   0.331    0.145    0.456 

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: 245
Number of extensions: 11
Number of successful extensions: 1
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: 252
Length of database: 282
Length adjustment: 25
Effective length of query: 227
Effective length of database: 257
Effective search space:    58339
Effective search space used:    58339
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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