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_004143815.1 Mesci_4656 polar amino acid ABC transporter inner membrane subunit

Query= uniprot:Q31RP0
         (377 letters)



>NCBI__GCF_000185905.1:YP_004143815.1
          Length = 395

 Score =  253 bits (645), Expect = 8e-72
 Identities = 147/380 (38%), Positives = 220/380 (57%), Gaps = 18/380 (4%)

Query: 8   QGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQSAGFNIGE 67
           +G F  D ++    +Q+LV++++  G  W+  N++ NL++  ++  F +L   AGF+I E
Sbjct: 13  RGSFINDPKIRGIFFQVLVVVLLVAGVWWIAHNVIDNLTRLRIASGFGFLKGRAGFDISE 72

Query: 68  SAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVA 127
           SAIAY +  +Y RA++VGL+N++ V  +G+I  T+IG + G+   S+NWL+R++   YV 
Sbjct: 73  SAIAYSSDSTYGRAILVGLLNTVIVAIVGIITATIIGFVIGIGRLSKNWLIRKICTVYVE 132

Query: 128 VVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLP---WPQTPGWLVVIL 184
           V RN P LL +  WY  +L  LPA +   +     +L+++G Y P   W     WL+ + 
Sbjct: 133 VFRNIPPLLVIFFWYSGVLAVLPAPRDSINLPFGSFLNQRGFYFPRAVWGDG-SWLIFV- 190

Query: 185 AIALVLFVSWLAQRQRSPRDWR--------WLYGAIAVVTVLMLLTQLSWPQQLQ-PGQ- 234
           A+ + + ++W   R+   R           W   A+ V   L+      +P     P Q 
Sbjct: 191 ALLVGIAMAWFVARKARQRQMATGQQFPVFWTSAALIVGLPLLAYALSGFPLSFDYPKQS 250

Query: 235 ---IRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLW 291
              + GG ++  EF +L L L  YT AFI EI+R GI  V AGQ EAA ALGL     L 
Sbjct: 251 TFNLTGGFQVRPEFLSLYLALSCYTAAFIAEIVRAGIRGVSAGQTEAAGALGLRSGSILR 310

Query: 292 QIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILML 351
            +VVPQA+R+++P L SQY+   KNSSLAIA+GYPDL ATA T LNQTG+ VE  +I+M+
Sbjct: 311 LVVVPQAMRIVIPPLTSQYLNLTKNSSLAIAIGYPDLTATAGTVLNQTGQAVEGVVIMMV 370

Query: 352 TYLAINAVISAGMNGLQQRL 371
            YLAI+ + S  MN    ++
Sbjct: 371 IYLAISLLTSLVMNWFNAKM 390


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: 443
Number of extensions: 22
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: 377
Length of database: 395
Length adjustment: 30
Effective length of query: 347
Effective length of database: 365
Effective search space:   126655
Effective search space used:   126655
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.

Links

Downloads

Related tools

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