GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 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)



>FitnessBrowser__HerbieS:HSERO_RS08065
          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.

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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