GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtB' in Mesorhizobium ciceri WSM1271

Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate YP_004141766.1 Mesci_2580 binding-protein-dependent transport system inner membrane protein

Query= uniprot:Q31RP0
         (377 letters)



>NCBI__GCF_000185905.1:YP_004141766.1
          Length = 387

 Score =  195 bits (495), Expect = 2e-54
 Identities = 125/371 (33%), Positives = 205/371 (55%), Gaps = 29/371 (7%)

Query: 24  LLVLLVVGLGAIWLVDNLVY---NLSQRGLSLSFDWLDQSAGFNIGESAIAYRTADSYAR 80
           LL +L VG  A  ++  +V    NL+ +G++  FD+L +S G+++  S +     D Y  
Sbjct: 14  LLQVLYVGSIAAMVLAGIVIARRNLADQGITSGFDFLFKSTGWDVNFSLLPATANDPYWW 73

Query: 81  ALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIV 140
             ++G++N+L + ++GLIL T++GT+ G+A  S N L R L R YV + RN PL+LQ+  
Sbjct: 74  YFLIGIINTLFLGSVGLILATIVGTIVGLARTSSNDLARLLGRTYVDIFRNIPLILQVFF 133

Query: 141 WYFPILLSLP---AAQQPWHWLGSLYLSKQGIYLPWPQTPGWL---VVILAIALVLFVSW 194
           WY  I+  LP   +A + W +L    L+ +G+Y+P+P           +  IA ++  +W
Sbjct: 134 WY-AIITHLPTPRSAHEAWGFL----LTSRGLYIPFPNVGSAAFAAATVAVIAAIVLPAW 188

Query: 195 LAQR--------QRSPRDWRWLYGAIAVVTVLMLLTQL------SWPQQLQPGQIRGGLR 240
           L +         QR    +     A+A  T+++ L +L       +P  LQ   +RGGLR
Sbjct: 189 LGRTSLLAQPIGQRRTIQFAAAAAALACATIILALGRLPDTPLLDFPA-LQGLNLRGGLR 247

Query: 241 LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR 300
           +  EF  L + +  Y G++I EI+RGG  SV  GQ EAA +LGL+  +    + +P ALR
Sbjct: 248 IPPEFATLAIAIAIYGGSYIAEIVRGGFKSVGTGQVEAALSLGLSPWRVFTLVRLPLALR 307

Query: 301 VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI 360
            ++P L +QYV   K +++ IAVG+ D +     T+N +G+ +E   ILM  +LAIN  +
Sbjct: 308 AMLPILANQYVWLMKATTMGIAVGFTDFFMIVALTINHSGQTLEAIGILMAGFLAINLSL 367

Query: 361 SAGMNGLQQRL 371
           +A  N + + +
Sbjct: 368 AAVFNRINKAI 378


Lambda     K      H
   0.326    0.140    0.445 

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: 381
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: 377
Length of database: 387
Length adjustment: 30
Effective length of query: 347
Effective length of database: 357
Effective search space:   123879
Effective search space used:   123879
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: 50 (23.9 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