GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00900 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)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4987 Branched-chain
           amino acid transport ATP-binding protein LivG (TC
           3.A.1.4.1)
          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 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, 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