GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Shewanella amazonensis SB2B

Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= uniprot:Q88GX0
         (260 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  150 bits (380), Expect = 3e-41
 Identities = 88/236 (37%), Positives = 132/236 (55%), Gaps = 4/236 (1%)

Query: 21  IRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQVD 80
           + I+GL+  Y    VLR ++L + +GE   L GPSG GK+TL+R I  L+    GSI ++
Sbjct: 4   LSIQGLHSDYRGEQVLRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAIN 63

Query: 81  GIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMYL 140
           G  ++A     A  +  IGM+FQ + LFPH++V DN L     VR L ++    R    L
Sbjct: 64  GKTVSADGCFVAPEKRSIGMIFQDYALFPHLTVADNILF---GVRQLDKQSRSVRLEEML 120

Query: 141 SKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEM-VAEVLDVLV 199
           S V +E    +YP +LSGGQQQRV+IARAL  +P ++L DEP S +D ++  A +L++  
Sbjct: 121 SLVKLEGLGKRYPHELSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRA 180

Query: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAFL 255
            L    ++ + VTH    A   A+ +   E G+I++   P+  +  P T     FL
Sbjct: 181 ILKARNVSAVFVTHSKDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFL 236


Lambda     K      H
   0.322    0.137    0.395 

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: 204
Number of extensions: 10
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: 260
Length of database: 341
Length adjustment: 26
Effective length of query: 234
Effective length of database: 315
Effective search space:    73710
Effective search space used:    73710
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 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