GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Bacillus altitudinis 41KF2b

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate WP_008347408.1 BA79_RS16380 amino acid permease

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>NCBI__GCF_000691145.1:WP_008347408.1
          Length = 448

 Score =  359 bits (921), Expect = e-103
 Identities = 178/450 (39%), Positives = 275/450 (61%), Gaps = 5/450 (1%)

Query: 5   LQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMRQ 64
           + Q  LKR L NRH+QLIA+GG IGTGLFLGS   +Q AGPS+I  Y I G+  F +MR 
Sbjct: 1   MAQQELKRDLSNRHVQLIAIGGTIGTGLFLGSGKAIQLAGPSIIFAYLIVGMAIFFVMRA 60

Query: 65  LGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPGV 124
           LGE++  +    S +  A  Y G +  F++GW YW  +++ +MA++ AVG YV YW+  +
Sbjct: 61  LGELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWFD-I 119

Query: 125 PTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGH---GGP 181
           P W+ A++C   +   NL  VK +GE EFWFA+IKV+ ++ +I  G  LL+ G     GP
Sbjct: 120 PQWIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGP 179

Query: 182 QASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQVI 241
             +++NLWSHGG FP+G  G      +++F++ G+EL+G++AAE   PQK+IP A+N++ 
Sbjct: 180 -VTVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIP 238

Query: 242 YRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVYNS 301
            RIL FY+ ++ VLL + PW E++A  SPFV  F  IG  + A ++N VVLT+A S  NS
Sbjct: 239 LRILFFYVGAIFVLLCINPWTELSASESPFVKTFGLIGIPVAAGLINFVVLTSAASACNS 298

Query: 302 GVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALGLL 361
           G+++ SR+LY L+ Q   P +  ++++  VP  A+ +S +      +++ LIP +A G++
Sbjct: 299 GMFSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLIPEQAFGIV 358

Query: 362 MALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVILAM 421
             +     +  W++I + HLK ++      +   FK+ + P  N   L   A ILVI+  
Sbjct: 359 TTISAICFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFAAILVIMLF 418

Query: 422 TPGLSVSVLLVPLWLVVMWAGYAFKRRRAA 451
                 ++LL P+W   ++  YA K+RR+A
Sbjct: 419 ADATRPALLLTPVWFGFLFLIYARKKRRSA 448


Lambda     K      H
   0.327    0.140    0.440 

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: 486
Number of extensions: 24
Number of successful extensions: 4
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: 461
Length of database: 448
Length adjustment: 33
Effective length of query: 428
Effective length of database: 415
Effective search space:   177620
Effective search space used:   177620
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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