GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00900 in Pseudomonas fluorescens FW300-N2E3

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO353_17110 AO353_17110 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_17110 AO353_17110 ABC
           transporter ATP-binding protein
          Length = 255

 Score =  127 bits (318), Expect = 3e-34
 Identities = 80/255 (31%), Positives = 138/255 (54%), Gaps = 20/255 (7%)

Query: 6   NKVLLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGN 65
           ++ +L+V+GL + +GG+ AV  V   V+E ++VS+IG NGAGKTT    +TG      G 
Sbjct: 2   SREILKVEGLSMRFGGLLAVNSVALSVKEKQVVSMIGPNGAGKTTVFNCLTGFYKPTAGT 61

Query: 66  IEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKM 125
           I+  G++I+G     +  +G+V   +   +F  MT  ENL +  + R      LA + K 
Sbjct: 62  IQLNGEAIEGLPGHKIAGKGVVRTFQNVRLFKEMTAVENLLIAQH-RHLNTNFLAGLFKT 120

Query: 126 FTIFPR-----------------LRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDE 168
              F R                 L+E  ++ AGT++ G+Q+ L + R +M++P +L+LDE
Sbjct: 121 -PAFRRSEREAMEYAEFWLDKVNLKEFANRPAGTLAYGQQRRLEIARCMMTRPSILMLDE 179

Query: 169 PSMGLSPIMVDKIFEVVRDV-YALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQ 227
           P+ GL+P   D +  ++  +     VT++L+E +    ++I+D  +V+  G     G  +
Sbjct: 180 PAAGLNPRETDDLKALIGTLREEHNVTVLLIEHDMKLVMSISDHIFVINQGTPLANGTPE 239

Query: 228 QLLNDPKVRAAYLGE 242
           Q+ ++P+V  AYLGE
Sbjct: 240 QIRDNPEVIKAYLGE 254


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: 134
Number of extensions: 7
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: 242
Length of database: 255
Length adjustment: 24
Effective length of query: 218
Effective length of database: 231
Effective search space:    50358
Effective search space used:    50358
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