GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4626
          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.

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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