GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1692 in Herbaspirillum seropedicae SmR1

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate HSERO_RS00900 HSERO_RS00900 amino acid ABC transporter ATPase

Query= uniprot:A0A165KC78
         (242 letters)



>FitnessBrowser__HerbieS:HSERO_RS00900
          Length = 241

 Score =  326 bits (835), Expect = 3e-94
 Identities = 168/236 (71%), Positives = 199/236 (84%), Gaps = 2/236 (0%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTL--SMNDGNI 66
           +L+V+ L VAYGGIQAVKG+D EV EGELV+LIG+NGAGKTTT+KAITGTL  S  +G+I
Sbjct: 5   ILKVQQLSVAYGGIQAVKGIDLEVNEGELVTLIGANGAGKTTTLKAITGTLPASRVEGHI 64

Query: 67  EYLGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIRKDKAGILADIEKMF 126
           EYLG+ +KGK +++LVK+ L MVPEGRGVF RM+I ENL MGAY   DK  I ADI+K F
Sbjct: 65  EYLGQPLKGKKSFELVKDKLAMVPEGRGVFTRMSIQENLLMGAYTSDDKGQIAADIDKWF 124

Query: 127 TIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFEVVR 186
            +FPRL+ER  Q+AGT+SGGEQQMLAM RALMS PK+LLLDEPSMGLSPIMV+KIFEV+R
Sbjct: 125 AVFPRLKERAAQMAGTLSGGEQQMLAMARALMSHPKLLLLDEPSMGLSPIMVEKIFEVIR 184

Query: 187 DVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLGE 242
           +V A G+TI+LVEQNA  AL  A RGYVMESGLITM G  QQ+L+DP+V+AAYLGE
Sbjct: 185 NVSAQGITILLVEQNAKLALEAAHRGYVMESGLITMQGQAQQMLDDPRVKAAYLGE 240


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: 237
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: 241
Length adjustment: 23
Effective length of query: 219
Effective length of database: 218
Effective search space:    47742
Effective search space used:    47742
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.

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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