GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Herbaspirillum seropedicae SmR1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS08925 HSERO_RS08925 amino acid ABC transporter ATPase

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__HerbieS:HSERO_RS08925
          Length = 242

 Score =  240 bits (612), Expect = 2e-68
 Identities = 121/237 (51%), Positives = 171/237 (72%), Gaps = 4/237 (1%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L +  L  AYG ++ + G+  EV +G++V+LIGSNGAGKTTTM+AI+G +    G +  
Sbjct: 1   MLTISNLHAAYGKVEVLHGISMEVPKGKVVTLIGSNGAGKTTTMRAISGMIKPKGGEVTL 60

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIR----KDKAGILADIEK 124
            GK+I G  +  + + GL   PEGR VFA M++T+NL +GA+ R    + K  I  D+E+
Sbjct: 61  GGKNITGLDSHKIARFGLAHSPEGRRVFATMSVTDNLLLGAFPRFTRARPKGDIAHDLER 120

Query: 125 MFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEV 184
              +FPRL+ER+ QLAGT+SGGEQQMLAM RA+M  P+V+LLDEPSMGL+PI+VD++F +
Sbjct: 121 ALELFPRLKERQSQLAGTLSGGEQQMLAMARAVMLNPEVILLDEPSMGLAPILVDEVFRI 180

Query: 185 VRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
           +  +   GVT++LVEQ A+ AL +AD GYV+E+G I++ GP  +L NDP V+AAYLG
Sbjct: 181 IVRLKEQGVTMLLVEQFAAAALNVADYGYVLENGKISVHGPADKLQNDPAVKAAYLG 237


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: 192
Number of extensions: 5
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: 242
Length of database: 242
Length adjustment: 23
Effective length of query: 219
Effective length of database: 219
Effective search space:    47961
Effective search space used:    47961
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: 46 (22.3 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 (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