GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artJ in Marinobacter adhaerens HP15

Align Putative ABC transporter arginine-binding protein 2 (characterized)
to candidate GFF2974 HP15_2918 glutamine ABC transporter, periplasmic glutamine-binding protein

Query= SwissProt::P30859
         (243 letters)



>FitnessBrowser__Marino:GFF2974
          Length = 252

 Score =  120 bits (302), Expect = 2e-32
 Identities = 79/247 (31%), Positives = 130/247 (52%), Gaps = 16/247 (6%)

Query: 3   KVLIAALIAGFSLSATAAETIRFATEASYPPFESIDANN-QIVGFDVDLAQALCKEIDAT 61
           K + A+L    +    +AET+R  T+ S+ PFE +D    +++GFD+++ + +       
Sbjct: 7   KTVSASLALTVAAGTVSAETLRVVTDPSFVPFEMMDQETGEMIGFDMEIIREVADRAGFE 66

Query: 62  CTFSNQAFDSLIPSLKFRRVEAVMAGMDITPEREKQVLFTTPYYDNSALFVGQQGK--YT 119
              +   F+ +IP+L+   V+  +AG+ IT ERE+ V F+ PYYD+    + ++G    +
Sbjct: 67  IDLNTMDFNGIIPALQTGNVDIAIAGITITEEREEIVDFSDPYYDSGLRILVREGNDDVS 126

Query: 120 SVDQLKGKKVGVQNGTTHQKFI---MDKHPEITTVPYDSYQNAKLDLQNGRIDGVFGDTA 176
             D L+GKK+G + G+T   ++   +D    +T  PY    +  + L +  ID VF D  
Sbjct: 127 EFDDLEGKKIGTKIGSTSYDYLVKNLDADDGVT--PYPGSSDMYMALMSRAIDAVFYDAP 184

Query: 177 VVTEW--LKDNPKLAAVGDKVTDKDYFGTGLGIAVRQGNTELQQKLNTALEKVKKDGTYE 234
            V  +   K   K+  VG       Y G   GIA++ G +E    +N AL  +K+DGTY+
Sbjct: 185 NVGYFARTKGEGKVTTVGPL-----YEGQQYGIALKSG-SEWVDDVNEALAAMKEDGTYK 238

Query: 235 TIYNKWF 241
           TIY KWF
Sbjct: 239 TIYEKWF 245


Lambda     K      H
   0.316    0.133    0.380 

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: 187
Number of extensions: 13
Number of successful extensions: 5
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: 243
Length of database: 252
Length adjustment: 24
Effective length of query: 219
Effective length of database: 228
Effective search space:    49932
Effective search space used:    49932
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 46 (22.3 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