GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proY in Pantoea rwandensis LMG 26275

Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate WP_084931869.1 HA51_RS03435 amino acid permease

Query= SwissProt::P46349
         (469 letters)



>NCBI__GCF_002095475.1:WP_084931869.1
          Length = 474

 Score =  404 bits (1039), Expect = e-117
 Identities = 212/454 (46%), Positives = 291/454 (64%), Gaps = 9/454 (1%)

Query: 12  LKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEMSAVNP 71
           LKTRH++M+++ GVIGAGLFVGS +VI STGPGA ++Y + G++V  IMRMLGEM+A  P
Sbjct: 15  LKTRHISMLALGGVIGAGLFVGSSAVIASTGPGAFITYLITGIMVALIMRMLGEMAAARP 74

Query: 72  TSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLWLTSLIL 131
             GSF +YA  A G  AGF  GWLYW+FWVIV+  EA+ G  II  W  ++P+WL SL L
Sbjct: 75  LKGSFVEYARLAFGNAAGFATGWLYWYFWVIVVGFEAVVGGQIIHGWTPELPVWLISLGL 134

Query: 132 TIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFSNLTGKG 191
            I++T  N+ SV+SFGE EYWF+ IKVV I+ FL+V  A++    P S    FSNLT +G
Sbjct: 135 MILMTSLNLLSVRSFGEAEYWFAGIKVVAIVIFLLVAGAYVLHLFPHS-TANFSNLTSQG 193

Query: 192 GFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIVFYVGSI 251
           GFFP G  ++  G+V VIFS  G E+  IAA E+ +P E++ KA  +V+ RI+VF+V + 
Sbjct: 194 GFFPHGAGTLFTGVVTVIFSMTGVEVATIAAAESEHPAENIRKAVNTVMVRILVFFVLAT 253

Query: 252 AIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYTTSRMLYS 311
            ++V   PW      +S FV   + IG+P +  ++  ++L AVLS LN+GLYT+SR+L  
Sbjct: 254 FLIVVAQPWTDVVPGKSAFVTTFDKIGIPGSGTMLTIVILVAVLSVLNAGLYTSSRLLAV 313

Query: 312 LAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSSGAIALLV 371
           L+   EAP    + SK+GVP  A++  T   Y AVV+    PDTVFLFL+NSSGA+ L V
Sbjct: 314 LSSNGEAPAWMAQRSKRGVPSLAVITSTLVGYAAVVIAALWPDTVFLFLLNSSGAVFLFV 373

Query: 372 YLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFIDSMRDELLL 431
           YL+I +SQLK+RK  E  +   LK +MW  P++  L   ++  +LVSMA     R  LL 
Sbjct: 374 YLMICLSQLKLRKTWE--HEGTLKFRMWGHPWIPLLVTASVIAVLVSMAVDADKRLSLLQ 431

Query: 432 TGVITGIVLISYLVF------RKRKVSEKAAANP 459
           + +   ++L SY V        +R+  E  A  P
Sbjct: 432 SILALMVILTSYAVLLFARSRSQRRTREIRAGRP 465


Lambda     K      H
   0.326    0.140    0.417 

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: 593
Number of extensions: 26
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: 469
Length of database: 474
Length adjustment: 33
Effective length of query: 436
Effective length of database: 441
Effective search space:   192276
Effective search space used:   192276
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