GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Rhizorhabdus wittichii RW1

Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein

Query= CharProtDB::CH_003736
         (237 letters)



>NCBI__GCF_000016765.1:WP_041378948.1
          Length = 252

 Score =  107 bits (267), Expect = 2e-28
 Identities = 71/224 (31%), Positives = 114/224 (50%), Gaps = 4/224 (1%)

Query: 5   MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64
           M+SFD V  HY     L +VSL I +G  V L+GA+GAGKTTLL  +       +G I  
Sbjct: 1   MISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAI 60

Query: 65  DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFF--AERDQFQERIKWVYE 122
           + +D+     A+ +R  +  V +G  +F  M+V EN+A+        R++   R+  + +
Sbjct: 61  EGRDVAAQPVAE-LRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLD 119

Query: 123 LFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQ 182
           L     +   +R   +SGG+ Q +   RAL + P ++L+DEP   L P+   ++      
Sbjct: 120 LVALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRA 179

Query: 183 LRE-QGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALL 225
           L E  G+T  +V  +  +AL LADR  V+  G ++      AL+
Sbjct: 180 LHEAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALI 223


Lambda     K      H
   0.321    0.137    0.390 

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: 166
Number of extensions: 10
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: 237
Length of database: 252
Length adjustment: 24
Effective length of query: 213
Effective length of database: 228
Effective search space:    48564
Effective search space used:    48564
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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