GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc02872 in Herbaspirillum seropedicae SmR1

Align N-Acetyl-D-glucosamine ABC transport system, permease component 1 (characterized)
to candidate HSERO_RS22740 HSERO_RS22740 ABC transporter permease

Query= reanno::Phaeo:GFF2751
         (308 letters)



>FitnessBrowser__HerbieS:HSERO_RS22740
          Length = 304

 Score =  366 bits (939), Expect = e-106
 Identities = 175/301 (58%), Positives = 225/301 (74%), Gaps = 1/301 (0%)

Query: 7   KPRRRWHIAVFLAPAVLVYTAIMIFPLFNTLRLALYSESDQ-IRQFVGLANFETLFGNPN 65
           K  R W +AV LAPAVL+Y      PL +TLRL  Y+ +D  +R FVGL N+ T+  +P+
Sbjct: 2   KTIRAWQLAVLLAPAVLIYALFSALPLLDTLRLGFYTANDAGVRSFVGLDNYRTILFDPD 61

Query: 66  WSEQFWNALGNNFWFFFVHMLVQNPIGVALAAILSHPRLRFAALYRTAIFVPTILSFVIV 125
           WS  FWNA+ NN  FF +HM +QNPIG+ LA + S   LR A  YRT IF+PT+LS VI+
Sbjct: 62  WSAAFWNAMWNNVKFFCIHMALQNPIGLLLATLFSLKGLRGARTYRTLIFLPTLLSVVII 121

Query: 126 GFAWKLILSPIWGITPDLLDAIGLKWLFAPWLGKEDYALTTLALISVWQFVGIPMMLIYA 185
           GF W+LILSP+WG+   LL  +GL   FAPWLG+E  AL TL+LISVWQ+VGIPMMLIYA
Sbjct: 122 GFIWQLILSPLWGVGEKLLGTVGLADWFAPWLGQESTALLTLSLISVWQYVGIPMMLIYA 181

Query: 186 ALLSIPEEVIEAGEVDGITGMSAFWKIKLPLILPSIGIISILTFVGNFNAFDLIYTTQGA 245
           ALL++PEEV+EA   +G + M  FW+IKLPLI P++G+++ILTFV NFNAFDLIY+ +GA
Sbjct: 182 ALLAVPEEVLEAAHAEGASAMRIFWQIKLPLIYPTLGLVTILTFVANFNAFDLIYSVKGA 241

Query: 246 LAGPDFSTDILGTFMYRTFFGFQLQLGDPHMGSAIATAMFAIILIGVCIYLFGIQTRLRR 305
           LAGP++++D+LGT+ YRTFFG+Q Q+G P MG+A+AT MF +IL GV  Y   +Q RL R
Sbjct: 242 LAGPNYASDLLGTYFYRTFFGYQAQIGSPTMGAAVATLMFLVILGGVGAYFVLVQRRLTR 301

Query: 306 Y 306
           Y
Sbjct: 302 Y 302


Lambda     K      H
   0.331    0.145    0.468 

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: 389
Number of extensions: 18
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: 308
Length of database: 304
Length adjustment: 27
Effective length of query: 281
Effective length of database: 277
Effective search space:    77837
Effective search space used:    77837
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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