GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Pantoea rwandensis LMG 26275

Align Aromatic amino acid:H+ symporter, AroP of 457 aas and 12 TMSs (Cosgriff and Pittard 1997). Transports phenylalanine, tyrosine and tryptophan (characterized)
to candidate WP_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter

Query= TCDB::P15993
         (457 letters)



>NCBI__GCF_002095475.1:WP_084934657.1
          Length = 463

 Score =  349 bits (896), Expect = e-101
 Identities = 179/456 (39%), Positives = 275/456 (60%), Gaps = 6/456 (1%)

Query: 1   MMEGQQHGEQLKRGLKNRHIQLIALGGAIGTGLFLGSASVIQSAGPGIILGYAIAGFIAF 60
           ++E +Q  E+L+R L NRHIQLIA+GGAIGTGLF+GS   I  AGP II  Y I GF+ F
Sbjct: 9   LIEAEQP-EKLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLF 67

Query: 61  LIMRQLGEMVVEEPVAGSFSHFAYKYWGSFAGFASGWNYWVLYVLVAMAELTAVGKYIQF 120
            +MR +GE+++      SFS FA    G +AG+ +GW YW  +V+  +A++ A+  Y Q 
Sbjct: 68  FVMRAMGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQL 127

Query: 121 WYPEIPTWVSAAVFFVVINAINLTNVKVFGEMEFWFAIIKVIAVVAMIIFGGWLL---FS 177
           W+P    W+SA +      A+N+  VK+FGEMEFWFAIIK++A+VA+II G  L+   + 
Sbjct: 128 WFPGFSIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYP 187

Query: 178 GNGGPQATVSNLWDQGGFLPHGFTGLVMMMAIIMFSFGGLELVGITAAEADNPEQSIPKA 237
              G  A++SN+WD GG  P G +G      I +F+F G+ELVG  AAE  +P + +P+A
Sbjct: 188 SPNGTTASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRA 247

Query: 238 TNQVIYRILIFYIGSLAVLLSLMPWTRVTADTSPFVLIFHELGDTFVANALNIVVLTAAL 297
            N +  RI++FY+ +L V++++ PW +V  + SPFV +F  +G    A+ +N VVLT+A 
Sbjct: 248 INAIPVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTSAA 307

Query: 298 SVYNSCVYCNSRMLFGLAQQGNAPKALASVDKRGVPVNTILVSALVTALCVLINYLAPES 357
           S  NS ++  SRMLFGLA+ G A KA   +  R VP   +  S L   + V + YL P+ 
Sbjct: 308 SSANSGIFSTSRMLFGLAELGVAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDV 367

Query: 358 AFGLLMALVVSALVIN--WAMISLAHMKFRRAKQEQGVVTRFPALLYPLGNWICLLFMAA 415
                M   VSA++    W +I  +++ +R+   ++   ++F   L     W+C+ F A 
Sbjct: 368 MTVFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMAFFAF 427

Query: 416 VLVIMLMTPGMAISVYLIPVWLIVLGIGYLFKEKTA 451
           VLV++ +      ++ + P+W ++L +G+L + + A
Sbjct: 428 VLVLLTLQEDTRQALMVTPLWFVILTLGWLLRRRKA 463


Lambda     K      H
   0.328    0.141    0.434 

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: 612
Number of extensions: 35
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: 457
Length of database: 463
Length adjustment: 33
Effective length of query: 424
Effective length of database: 430
Effective search space:   182320
Effective search space used:   182320
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