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_4626 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)

Query= uniprot:A0A165KC78
         (242 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4626 Branched-chain
           amino acid transport ATP-binding protein LivF (TC
           3.A.1.4.1)
          Length = 278

 Score =  209 bits (533), Expect = 4e-59
 Identities = 112/244 (45%), Positives = 160/244 (65%), Gaps = 7/244 (2%)

Query: 5   SNKVLLQVKGLKVAYGGIQAV-KGVDFEVREGELVSLIGSNGAGKTTTMKAITGTL---- 59
           S  ++L V G++V Y  +  V KGV  +V +G +V+++G NGAGKTTT++AI+  L    
Sbjct: 12  SKNIVLNVNGIEVIYNHVILVLKGVSLQVPQGSIVAILGGNGAGKTTTLRAISNLLQGER 71

Query: 60  -SMNDGNIEYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGI 118
            ++  G+IE  G+ I+     DLV+ G+V V EGR  FA +TI ENL  G+Y R  KA I
Sbjct: 72  GAVTKGSIELRGERIENLSPADLVQRGVVQVMEGRHCFAHLTIEENLMTGSYTRTSKAEI 131

Query: 119 LADIEKMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMV 178
            A++EK++  FPRL+ R+   A   SGGEQQM A+GRALM+ P ++LLDEPSMGL+P +V
Sbjct: 132 AANLEKVYNYFPRLKTRRTSQAAYTSGGEQQMCAIGRALMANPSMVLLDEPSMGLAPQIV 191

Query: 179 DKIFEVVRDVYAL-GVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRA 237
           +++F +V+D+     VT +L EQN + AL  +D GY+MESG + M G    L N+  V+ 
Sbjct: 192 EEVFNIVKDLNTKEKVTFLLAEQNTNMALKYSDYGYIMESGRVVMDGAASDLANNEDVKE 251

Query: 238 AYLG 241
            YLG
Sbjct: 252 FYLG 255


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: 166
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: 242
Length of database: 278
Length adjustment: 24
Effective length of query: 218
Effective length of database: 254
Effective search space:    55372
Effective search space used:    55372
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.

Links

Downloads

Related tools

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