GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_17605 in Shewanella sp. ANA-3

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= uniprot:A0A1N7U8S3
         (276 letters)



>lcl|FitnessBrowser__ANA3:7026050 Shewana3_3192 sulfate ABC
           transporter, ATPase subunit (RefSeq)
          Length = 376

 Score =  139 bits (349), Expect = 1e-37
 Identities = 89/255 (34%), Positives = 150/255 (58%), Gaps = 22/255 (8%)

Query: 25  IKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVIT 84
           + +++  I K++G+ + L  ++L+ ++G++I L+G SGSGK+T+LR I  LE  D+G I 
Sbjct: 1   MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60

Query: 85  LDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMA----PRRV 140
                        G R   Q  +++   R+  VFQ++ L+ HMTV +N+       P++ 
Sbjct: 61  F------------GNRDVTQVHVRD--RRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQ 106

Query: 141 LDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPT 200
              S AE +KR    L+ V L   +A +YP  LSGGQ+QR+A+ARALA +PE++L DEP 
Sbjct: 107 RP-SKAEIQKRVSHLLEMVQL-GHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPF 164

Query: 201 SALDPELVGEVLKVIQTLAEEGR-TMLMVTHEMGFARQVSSQVLFLHQGRVEE-HGDARI 258
            ALD ++  E+ + +++L +E + T + VTH+   A ++S +V+ +  G +E+ +    +
Sbjct: 165 GALDAKVRKELRRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIEL 224

Query: 259 LDQPNSERLQQFLSN 273
             QPNS  +  FL N
Sbjct: 225 YAQPNSRFVFDFLGN 239


Lambda     K      H
   0.319    0.133    0.372 

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: 212
Number of extensions: 9
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: 276
Length of database: 376
Length adjustment: 28
Effective length of query: 248
Effective length of database: 348
Effective search space:    86304
Effective search space used:    86304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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