GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00870 in Herbaspirillum seropedicae SmR1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS08065 HSERO_RS08065 branched-chain amino acid ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS08065 HSERO_RS08065
           branched-chain amino acid ABC transporter
           substrate-binding protein
          Length = 394

 Score =  223 bits (569), Expect = 5e-63
 Identities = 126/384 (32%), Positives = 203/384 (52%), Gaps = 14/384 (3%)

Query: 2   QLKLKLTVVAAIAAAAGVASAQEQV----------VKIGHVAPVSGAQAHYGKDNENGAR 51
           +L   L  +A + A  G A+AQ +           + IG   P+SG     GK  +NG +
Sbjct: 6   RLLAALLALATLGAPVG-ATAQPRAPLPDRQETATLAIGFAGPLSGPSGGVGKSMQNGVQ 64

Query: 52  MAIEELNAQGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIP 111
           +A+ E N +G+ IGGK  +  L+A+DD ADP      A+ L   +V  VVGH  SGT++ 
Sbjct: 65  LALAEANRRGLRIGGKSWQLRLIAQDDRADPATAEFVARSLVQQQVIAVVGHWTSGTSLA 124

Query: 112 ASKVYNDCGIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAII 171
           A+ VY+  G+  VT +A +  LT   Y   FR I N+ +LG   A YAVD L+ +T+  I
Sbjct: 125 AAPVYHRAGVIQVTPSAMSRRLTAMSYPRIFRTIPNNESLGRLAAGYAVDKLETRTIVTI 184

Query: 172 DDRTAYGQGVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDP 231
           DDRT +GQG+A+ F +TA+ +G +VV     +DK +DF A L   +   PD IF+GG+D 
Sbjct: 185 DDRTPFGQGLAEQFARTASERGAQVVGRYSVSDKTSDFNAALLEARKLQPDLIFFGGLDW 244

Query: 232 QGGPMLRQMEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTA 291
           Q G + + + +L + + +     G  T  +  L          +  E G    KMPG  +
Sbjct: 245 QAGVLAKSIRRLKL-HARLMASPG--TLGLPFLMRAGPDANGALVLEPGPPQDKMPGWKS 301

Query: 292 WKAKYDAKYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAF 351
           ++ +Y   + +   +Y+ + Y+A   I+  +++A S DP+     + +  F+GV+  +AF
Sbjct: 302 FRQRYSENFDSDMDLYAVFAYEAAQAIIQGIRQAGSADPERIAEAMHRLRFEGVSGPVAF 361

Query: 352 EPNGEMKNPAITLYVYKDGKKTPL 375
              G++  P+ T+Y  KD +  P+
Sbjct: 362 NEEGDLLQPSFTMYEVKDQRWQPV 385


Lambda     K      H
   0.315    0.131    0.375 

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: 322
Number of extensions: 15
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: 375
Length of database: 394
Length adjustment: 30
Effective length of query: 345
Effective length of database: 364
Effective search space:   125580
Effective search space used:   125580
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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 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, 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