GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pantoea rwandensis LMG 26275

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

Query= uniprot:Q4KIP0
         (466 letters)



>NCBI__GCF_002095475.1:WP_084934657.1
          Length = 463

 Score =  351 bits (901), Expect = e-101
 Identities = 184/455 (40%), Positives = 272/455 (59%), Gaps = 14/455 (3%)

Query: 9   ELKRGLKNRHIQLIALGGAIGTGLFLGSAGVLKSAGPSMILGYAIAGFIAFLIMRQLGEM 68
           +L+R L NRHIQLIA+GGAIGTGLF+GS   +  AGPS+I  Y I GF+ F +MR +GE+
Sbjct: 17  KLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRAMGEL 76

Query: 69  IVEEPVAGSFSHFAHKYWGGYFGFLAGWNYWVLYVLVGMAELTAVGKYVQFWWPEIPTWV 128
           ++      SFS FA    G + G+  GW YW  +V+ G+A++ A+  Y Q W+P    W+
Sbjct: 77  LLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPGFSIWM 136

Query: 129 SAAVFFVLVNLINMMNVKFFGEAEFWFAIIKVVAIVGMIVLGCYML---FSGSGGSQASV 185
           SA +       +N+  VK FGE EFWFAIIK+VAIV +I+ G  ++   +    G+ AS+
Sbjct: 137 SALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYPSPNGTTASL 196

Query: 186 SNLWSHGGFFPNGGTGLLMAMAFIMFSFGGLELVGITAAEAAEPRKVIPKAINQVVYRVL 245
           SN+W HGG FP G +G        +F+F G+ELVG  AAE  +P KV+P+AIN +  R++
Sbjct: 197 SNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRAINAIPVRII 256

Query: 246 IFYVGALAVLLSLYPWDELLVSLNAGGDAYSSSPFVKIFSLIGSDAAAQILNFVVLTAAL 305
           +FYV AL V++++ PW+++L          + SPFV++F LIG  AAA I+NFVVLT+A 
Sbjct: 257 MFYVLALLVIMAVTPWNQVLP---------NRSPFVEMFVLIGLPAAASIVNFVVLTSAA 307

Query: 306 SVYNSGVYCNSRMLYGLAEQGDAPKALMKLNKQGVPILALGISALITLLCVLVNYLAPHE 365
           S  NSG++  SRML+GLAE G A KA  +L+ + VP   L  S L  L+ V + YL P  
Sbjct: 308 SSANSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDV 367

Query: 366 ALELLFALVVAAL--MINWALISLTHLRFRKAMAEQGVVPSFKAFWSPLSNYLCLAFMVM 423
                    V+A+  M  W +I  ++L +RK   ++     FK        ++C+AF   
Sbjct: 368 MTVFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMAFFAF 427

Query: 424 IVGVMWMIPGIRASVYAIPVWVLVIWGFYLLSRAK 458
           ++ ++ +    R ++   P+W +++   +LL R K
Sbjct: 428 VLVLLTLQEDTRQALMVTPLWFVILTLGWLLRRRK 462


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: 686
Number of extensions: 40
Number of successful extensions: 5
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: 463
Length adjustment: 33
Effective length of query: 433
Effective length of database: 430
Effective search space:   186190
Effective search space used:   186190
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