GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1692 in Pseudomonas fluorescens GW456-L13

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PfGW456L13_4611 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= uniprot:A0A165KC78
         (242 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4611
           Branched-chain amino acid transport ATP-binding protein
           LivF (TC 3.A.1.4.1)
          Length = 233

 Score =  245 bits (626), Expect = 5e-70
 Identities = 119/233 (51%), Positives = 174/233 (74%), Gaps = 1/233 (0%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +LQ + +   YG IQA+  V+ EVR+GE+V+LIG+NGAGK+T +  + G+   + G+I Y
Sbjct: 1   MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPRAHSGSIRY 60

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMFTI 128
           +G+ + G+ +  ++++ + +VPEGR VF+R+T+ ENL MG +    K      ++K+  +
Sbjct: 61  MGEELVGQDSSQIMRKSIAVVPEGRRVFSRLTVEENLSMGGFFTA-KGDYQEQMDKVLGL 119

Query: 129 FPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVRDV 188
           FPRL+ER +Q  GTMSGGEQQMLA+GRALMS+PK+LLLDEPS+GL+PI++ +IF+++  +
Sbjct: 120 FPRLKERFNQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQL 179

Query: 189 YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
              GVT+ LVEQNA++AL IADR YV+E+G + MTG G+ LL DPKVR AYLG
Sbjct: 180 RKDGVTVFLVEQNANQALKIADRAYVLENGRVVMTGTGEALLTDPKVRDAYLG 232


Lambda     K      H
   0.317    0.136    0.373 

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: 211
Number of extensions: 10
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: 242
Length of database: 233
Length adjustment: 23
Effective length of query: 219
Effective length of database: 210
Effective search space:    45990
Effective search space used:    45990
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: 41 (21.7 bits)
S2: 46 (22.3 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