GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Pseudomonas stutzeri RCH2

Align D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized)
to candidate GFF1660 Psest_1697 Gamma-aminobutyrate permease and related permeases

Query= TCDB::M1IW84
         (556 letters)



>FitnessBrowser__psRCH2:GFF1660
          Length = 464

 Score =  327 bits (839), Expect = 5e-94
 Identities = 182/454 (40%), Positives = 268/454 (59%), Gaps = 17/454 (3%)

Query: 17  LRRDLANRHIQLIAIGGAIGTGLFMGSGRTISLAGPAVMVVYGIIGFFVFFVLRAMGELL 76
           L+R L NRHIQLIA+GGAIGTGLF+GS   +  AGP++++ Y I GF  F ++R +GE++
Sbjct: 11  LQRGLKNRHIQLIALGGAIGTGLFLGSAGVLRSAGPSMILGYAIGGFIAFLIMRQLGEMI 70

Query: 77  LSNLNYKSFVDFAADLLGPAAGFFVGWSYWFAWVVTGIADLVAITSYARFWWPGLPIWVP 136
           +      SF  FA    G  AGF  GW+YW  +V+ G+A+L A+  Y +FWWP +P W  
Sbjct: 71  VEEPVAGSFSHFAHKYGGGYAGFLSGWNYWVLYVLVGMAELTAVGKYVQFWWPEVPTWAT 130

Query: 137 ALVTVALILAVNLFSVRHFGELEFWFALIKVAAIVCLIAVGAILVATNFVSPHGVHATIE 196
           A     LI  +NL +V+ FGE EFWFA++KVAAIV +I +G  L+ +      G  A+I 
Sbjct: 131 AAAFFVLINLINLSNVKAFGETEFWFAIVKVAAIVGMILLGLFLLVS---GKGGEQASIS 187

Query: 197 NLWNDNGFFPTGFLGVVSGFQIAFFAYIGVELVGTAAAETADPRRTLPRAINAVPLRVAV 256
           NLW+  GFFP GF G++    I  F++ G+ELVG  AAE A+P+  +P+AIN V  R+ +
Sbjct: 188 NLWSHGGFFPNGFSGMLLALAIIMFSFGGLELVGITAAEAAEPKTVIPKAINQVVYRILI 247

Query: 257 FYIGALLAILAVVPWRQF-----ASGE----SPFVTMFSLAGLAAAASVVNFVVVTAAAS 307
           FYIGAL  +LA+ PW        A+G+    SPFV +FSL G   AA ++NFVV+TAA S
Sbjct: 248 FYIGALTVLLALYPWDALLLTLGAAGDPYSGSPFVQIFSLIGSDTAAHLLNFVVLTAALS 307

Query: 308 SANSGFFSTGRMLFGLADEGHAPAAFHQLNRGGVPAPALLLTAPLLLTSIPLLYAGRSVI 367
             NSG +   RML+GLA++G AP +  ++N  GVP  A+ ++A + L  + + Y      
Sbjct: 308 VYNSGVYCNSRMLYGLAEQGDAPRSLMKINSRGVPVLAVGVSALVTLLCVAVNYLFPQ-- 365

Query: 368 GAFTLVTTVSSLLFMFVWAMIIISYLVYRRRHPQRHTDSVYKMPGGVVMCWAVLVFFAFV 427
           GA  L+ +++    +  WAMI +++L +RR   Q+  +  +K     +  +  L F A +
Sbjct: 366 GALELLMSLAVAALVINWAMISLAHLKFRRAMQQQGVEPSFKAFWFPLSNYLCLAFVAGI 425

Query: 428 IWTLTTETETATALAWFPLWFVLLAVGWLVTQRR 461
           +  +        ++   P+W   L   WL  + R
Sbjct: 426 LIIMLWLPGIRMSVFAIPVWVGFL---WLCYRLR 456


Lambda     K      H
   0.328    0.140    0.442 

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: 694
Number of extensions: 34
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: 556
Length of database: 464
Length adjustment: 34
Effective length of query: 522
Effective length of database: 430
Effective search space:   224460
Effective search space used:   224460
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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