GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Bacillus altitudinis 41KF2b

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

Query= uniprot:Q4KIP0
         (466 letters)



>NCBI__GCF_000691145.1:WP_008347408.1
          Length = 448

 Score =  369 bits (948), Expect = e-107
 Identities = 191/462 (41%), Positives = 281/462 (60%), Gaps = 16/462 (3%)

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

Query: 65  LGEMIVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWPEI 124
           LGE+++ +    S +  A  Y G +  F+ GW YW  +++  MA++ AVG YVQ+W+ +I
Sbjct: 61  LGELLLSKAGYQSLTDIAEDYLGPWASFVTGWTYWFCWIMTAMADVIAVGVYVQYWF-DI 119

Query: 125 PTWVSAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYMLFSG--SGGSQ 182
           P W+ A +  +++   N++ VK FGE EFWFA+IKV+ I+ +I +G  +L  G  +    
Sbjct: 120 PQWIPAIICLLILLGFNLLTVKLFGEMEFWFALIKVITILLLIGVGIVLLIIGFQTDAGP 179

Query: 183 ASVSNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVY 242
            +V+NLWSHGG FPNG TG L++   ++F++ G+ELVG++AAE A P+K IP AIN++  
Sbjct: 180 VTVTNLWSHGGLFPNGVTGFLLSFQMVIFAYVGVELVGVSAAETANPQKNIPSAINKIPL 239

Query: 243 RVLIFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLT 302
           R+L FYVGA+ VLL + PW EL         + S SPFVK F LIG   AA ++NFVVLT
Sbjct: 240 RILFFYVGAIFVLLCINPWTEL---------SASESPFVKTFGLIGIPVAAGLINFVVLT 290

Query: 303 AALSVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLA 362
           +A S  NSG++  SR+LY L+ Q   P +  +LNK  VP  AL +S ++  +  L++ L 
Sbjct: 291 SAASACNSGMFSTSRILYNLSHQKQGPASFGRLNKHAVPSNALFVSTIVVSVGALLSKLI 350

Query: 363 PHEALELLFALVVAALMINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMV 422
           P +A  ++  +     +  W++I + HL+++K   E     +FKA ++P  N   L    
Sbjct: 351 PEQAFGIVTTISAICFIWVWSIILICHLKYKKTRPELHKASTFKAPFTPFVNIAVLVLFA 410

Query: 423 MIVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAKKASQPA 464
            I+ +M      R ++   PVW    +GF  L  A+K  + A
Sbjct: 411 AILVIMLFADATRPALLLTPVW----FGFLFLIYARKKRRSA 448


Lambda     K      H
   0.327    0.141    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: 626
Number of extensions: 39
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: 466
Length of database: 448
Length adjustment: 33
Effective length of query: 433
Effective length of database: 415
Effective search space:   179695
Effective search space used:   179695
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