GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__HerbieS:HSERO_RS22740 HSERO_RS22740 ABC
           transporter permease
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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