GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livH in Cupriavidus basilensis 4G11

Align ABC transporter permease (characterized, see rationale)
to candidate RR42_RS16975 RR42_RS16975 ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>FitnessBrowser__Cup4G11:RR42_RS16975
          Length = 311

 Score =  412 bits (1058), Expect = e-120
 Identities = 209/311 (67%), Positives = 257/311 (82%), Gaps = 2/311 (0%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MDI +QQI+NGLVLGS+YALIALGYTMVYGI+ +INFAHG+VLMIGALT+ S I  +Q  
Sbjct: 1   MDIFIQQIVNGLVLGSIYALIALGYTMVYGILGIINFAHGDVLMIGALTALSAILGLQKF 60

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120
            PG P W+ L++AT+IA  V A L + IE+VAYRPLR++PRLAPLITAIG+SI+LQTLAM
Sbjct: 61  FPGLPEWLTLVIATLIAMPVCAALAYTIERVAYRPLRNAPRLAPLITAIGVSIILQTLAM 120

Query: 121 IIWKPNYKPYPTMLPSSPFEIG--GAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178
           +IW  N   +P +LPSSP +IG  GA IT  +I+I+G+  + +A L+ LVN T LGRAMR
Sbjct: 121 MIWSRNPLTFPQLLPSSPIDIGSTGATITGKEIVIIGMALMVMAGLLTLVNRTKLGRAMR 180

Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238
           ATAEN +VA LMGV P+ VISATF+IGA LAA+AG+M A+NYG A   MGF+PGLKAFTA
Sbjct: 181 ATAENQKVAGLMGVNPNFVISATFMIGAALAALAGVMMATNYGNAHFYMGFIPGLKAFTA 240

Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298
           AV GGIGNLAGA+VGG+LLGLIEA+G+GYIG LT G+ GS+Y D+FAFIVLII+L  RPS
Sbjct: 241 AVLGGIGNLAGAMVGGMLLGLIEALGAGYIGDLTNGVFGSNYQDVFAFIVLIIVLVFRPS 300

Query: 299 GLLGERVADRA 309
           G++GERV++RA
Sbjct: 301 GIMGERVSERA 311


Lambda     K      H
   0.327    0.142    0.419 

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: 319
Number of extensions: 8
Number of successful extensions: 2
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: 309
Length of database: 311
Length adjustment: 27
Effective length of query: 282
Effective length of database: 284
Effective search space:    80088
Effective search space used:    80088
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 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