GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Acidovorax sp. GW101-3H11

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_1936 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1936
          Length = 272

 Score =  213 bits (542), Expect = 3e-60
 Identities = 113/235 (48%), Positives = 154/235 (65%), Gaps = 1/235 (0%)

Query: 9   QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68
           QPLL++  VE+ YG I+A+ GV + V +GEI +++G+NGAGK+T++ TI G    R GS+
Sbjct: 18  QPLLRLQNVESAYGPIKAIRGVSLQVRRGEIAAVLGSNGAGKTTILKTISGIIDPRKGSI 77

Query: 69  VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKH-FAEDVEKIF 127
            F+G+DIT      I R  +   PEGR +FP ++V +NL MGA     K   A D+E +F
Sbjct: 78  EFQGQDITARDPAAIVRRGLMHVPEGREVFPLLSVRDNLLMGAYTRADKDGVARDIETVF 137

Query: 128 TLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIR 187
             FP LKER AQ  G LSGG+QQML+I RALMA P+L+LLDEPSLGL+P + K IFE + 
Sbjct: 138 GYFPILKERAAQDAGLLSGGQQQMLAISRALMAAPELILLDEPSLGLSPKLTKEIFEIVV 197

Query: 188 KLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           ++N   G T+ LVEQNA  AL  S   YV+ NG++ M  S + L    +++  YL
Sbjct: 198 RINRERGTTILLVEQNANMALNASDYGYVLENGRIVMEDSCERLREKDDIKEFYL 252


Lambda     K      H
   0.320    0.137    0.387 

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: 186
Number of extensions: 8
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: 247
Length of database: 272
Length adjustment: 24
Effective length of query: 223
Effective length of database: 248
Effective search space:    55304
Effective search space used:    55304
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:

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