GapMind for catabolism of small carbon sources

 

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

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_4987 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4987
          Length = 272

 Score =  213 bits (541), Expect = 4e-60
 Identities = 113/248 (45%), Positives = 168/248 (67%), Gaps = 7/248 (2%)

Query: 1   MAEKSNKVLLQVKGLKVAYGGI-QAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTL 59
           M + +   +L+V  ++V Y  + QA++G+   V  G++V+L+GSNGAGK+TT+KAI+G L
Sbjct: 1   MTQPTPAHVLEVNNIEVIYNKVVQALRGLSLAVPRGQIVALLGSNGAGKSTTLKAISGLL 60

Query: 60  SMNDGNIE-----YLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKD 114
           ++ DG +E     + G+         LV+ GL  V EGR VF  +T+ ENL    Y    
Sbjct: 61  ALEDGVVESGSIHFNGQPTAAVAPQQLVRNGLSHVMEGRRVFEDLTVEENLVAATYALTG 120

Query: 115 KAGILADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLS 174
           ++G   D + +++ FPRL ER+  LAG +SGGEQQMLA+GRAL++QP+++LLDEPS+GLS
Sbjct: 121 RSGTTPDFDLVYSYFPRLHERRKGLAGYLSGGEQQMLAIGRALIAQPQLILLDEPSLGLS 180

Query: 175 PIMVDKIFEVVRDVYA-LGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDP 233
           P +V+ IF ++  + A  G +++LVEQNA+ ALA+A RGY+ME+G I + G  ++L NDP
Sbjct: 181 PKLVEDIFTIIARINAERGTSMLLVEQNATVALAVAHRGYIMENGKIVIDGTAERLANDP 240

Query: 234 KVRAAYLG 241
            VR  YLG
Sbjct: 241 DVREFYLG 248


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: 201
Number of extensions: 12
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: 272
Length adjustment: 24
Effective length of query: 218
Effective length of database: 248
Effective search space:    54064
Effective search space used:    54064
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: 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