GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_17605 in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_00221 H281DRAFT_00221 amino acid ABC transporter ATP-binding protein, PAAT family

Query= uniprot:A0A1N7U8S3
         (276 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00221 H281DRAFT_00221 amino
           acid ABC transporter ATP-binding protein, PAAT family
          Length = 259

 Score =  323 bits (827), Expect = 3e-93
 Identities = 170/257 (66%), Positives = 200/257 (77%), Gaps = 2/257 (0%)

Query: 22  TAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAG 81
           T   KL V+ +HK+YG++EVLKGV+L A  GDVIS+IG+SGSGKSTMLRCINFLEQP+AG
Sbjct: 3   TTKQKLFVDELHKQYGDNEVLKGVTLKANAGDVISVIGSSGSGKSTMLRCINFLEQPNAG 62

Query: 82  VITLDGISIEMRQGRAGT-RAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRV 140
            I +DG  +  +  + G  R     QLQ +RT+L+MVFQHFNLWSHM VLENI  AP  V
Sbjct: 63  RIFVDGEEVRTQIAKNGALRVSDPKQLQRVRTKLSMVFQHFNLWSHMNVLENIVEAPVNV 122

Query: 141 LDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPT 200
           L +   EAE RAR YL+KVGL  R+  QYP+ LSGGQQQRVAIARALAM P+++LFDEPT
Sbjct: 123 LGLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMHPDVMLFDEPT 182

Query: 201 SALDPELVGEVLKVIQTLAEEGRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHGDA-RIL 259
           SALDPELVGEVLKV+QTLAEEGRTM++VTHEM FAR VS+ V+FLHQGRVEE G    + 
Sbjct: 183 SALDPELVGEVLKVMQTLAEEGRTMIVVTHEMAFARNVSNHVMFLHQGRVEEEGHPDEVF 242

Query: 260 DQPNSERLQQFLSNRLK 276
               SERL+QFLS  LK
Sbjct: 243 RNTRSERLKQFLSGSLK 259


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: 259
Number of extensions: 8
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: 259
Length adjustment: 25
Effective length of query: 251
Effective length of database: 234
Effective search space:    58734
Effective search space used:    58734
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: 47 (22.7 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 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