GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natH in Brucella inopinata BO1

Align NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate WP_008504345.1 BIBO1_RS07175 amino acid ABC transporter permease

Query= TCDB::Q8YPM7
         (381 letters)



>NCBI__GCF_000182725.1:WP_008504345.1
          Length = 385

 Score =  248 bits (633), Expect = 2e-70
 Identities = 153/405 (37%), Positives = 221/405 (54%), Gaps = 83/405 (20%)

Query: 6   WLRKNLFSTWYNSLLTVICSALSLWLVQGIIVW--------------ATTKAQ------- 44
           WLR NLF+T  ++ LT+    L +W V  II W                T AQ       
Sbjct: 29  WLRVNLFATPVDAALTIFGLVLVVWFVLPIIEWLFINAAWTGTSRTACLTAAQGGAQPDG 88

Query: 45  -----WAVIQVNLRLFLVGRFPQTEYWRVWIVLAIASTLGAVTAGIFFNQQKLTWRKVGL 99
                WA +      FL GR+P +E WRV                               
Sbjct: 89  WSGACWAFVNAKYEQFLYGRYPISERWRV------------------------------- 117

Query: 100 FAFIVGLLLILFTLDLSSRLWLLLTAVLLIPGFLLGSRLTNLVAPWLSLIWLLSFPIILW 159
                         DL++ ++  L   LLIP   +  +  N      ++++ L FP++ +
Sbjct: 118 --------------DLTALIFAALLVPLLIPK--VPKKGLN------AILFFLVFPVVAF 155

Query: 160 --LIGGGFGLRPVSSNLWNGLLLTLLMAAISIVLSFPIGVLLALGRTSNLPVVRWFSILY 217
             L+GG FGL  V + LW GLL+TL+++ + I +S P+G++LALGR S LPV++  SI++
Sbjct: 156 FLLVGGWFGLPYVETPLWGGLLVTLVLSFVGIAVSLPLGIVLALGRRSKLPVIKTLSIIF 215

Query: 218 IEIVRGVPLIGILFLAQVMLPLFFAADVRLDRVLRAIAGLVLFSAAYMAENVRGGLQAVS 277
           IE+VRGVPL+ +LF+A VMLPLF    V  D++LRA+ G+ LF++AYMAE VRGGLQA+ 
Sbjct: 216 IEMVRGVPLVTVLFMASVMLPLFLPPGVTFDKLLRALIGVALFASAYMAEVVRGGLQAIP 275

Query: 278 RGQVEAAKALGLNTFFVVLLIVLPQALRAVIPALVGQFIGLFKDTSLLSLVGLVELTGIA 337
           RGQ E A ALGL+ +    L+VLPQAL+ VIP +V  FIGLFKDTSL+ ++G+ +L GI 
Sbjct: 276 RGQYEGADALGLSYWQKTGLVVLPQALKLVIPGIVNTFIGLFKDTSLVYIIGMFDLLGIV 335

Query: 338 RSILAQPQFIGRY--AEVYLFIGLIYWLFCYSMSLASRRLERQLN 380
           R   +   +      A   +F G ++W+FC++MS  S  +ER+L+
Sbjct: 336 RQNFSDANWASPQTPATGLIFAGFVFWIFCFAMSRYSIFMERRLD 380


Lambda     K      H
   0.332    0.145    0.452 

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: 523
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 381
Length of database: 385
Length adjustment: 30
Effective length of query: 351
Effective length of database: 355
Effective search space:   124605
Effective search space used:   124605
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: 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