GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_04042 in Pantoea rwandensis LMG 26275

Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter

Query= uniprot:A0A2Z5MFR8
         (461 letters)



>NCBI__GCF_002095475.1:WP_084934657.1
          Length = 463

 Score =  364 bits (935), Expect = e-105
 Identities = 185/453 (40%), Positives = 273/453 (60%), Gaps = 7/453 (1%)

Query: 4   ALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFMIMR 63
           A Q + L+R L NRHIQLIA+GGAIGTGLF+GS   +  AGPS+I  Y I G + F +MR
Sbjct: 12  AEQPEKLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMR 71

Query: 64  QLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYWWPG 123
            +GE++       SFS FA    G + G+ +GW YW  +V+  +A++ A+  Y   W+PG
Sbjct: 72  AMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPG 131

Query: 124 VPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGH----G 179
              W+SAL+C     A+N+A VK +GE EFWFAIIK+VA++ +I+  G +LVS H     
Sbjct: 132 FSIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALII-TGIVLVSMHYPSPN 190

Query: 180 GPQASISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQ 239
           G  AS+SN+W HGG FP G  G F    + +F+F G+EL+G  AAE  +P K +P+A+N 
Sbjct: 191 GTTASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRAINA 250

Query: 240 VIYRILIFYICSLAVLLSLYPWNEVAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSVY 299
           +  RI++FY+ +L V++++ PWN+V    SPFV +F  IG    A+++N VVLT+A S  
Sbjct: 251 IPVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTSAASSA 310

Query: 300 NSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEALG 359
           NSG+++ SRML+GLAE G A +A  ++  R VP   +  S L     V + YLIP     
Sbjct: 311 NSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDVMTV 370

Query: 360 LLMALVVAALVLN--WALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILV 417
             M   V+A++    W +I  ++L  R+          FK        W+C+AF A +LV
Sbjct: 371 FTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMAFFAFVLV 430

Query: 418 ILAMTPGLSVSVLLVPLWLVVMWAGYAFKRRRA 450
           +L +      ++++ PLW V++  G+  +RR+A
Sbjct: 431 LLTLQEDTRQALMVTPLWFVILTLGWLLRRRKA 463


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: 524
Number of extensions: 23
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: 461
Length of database: 463
Length adjustment: 33
Effective length of query: 428
Effective length of database: 430
Effective search space:   184040
Effective search space used:   184040
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