GapMind for catabolism of small carbon sources

 

Alignments for a candidate for larD in Pseudomonas stutzeri RCH2

Align D/L-lactic acid transporter; Lactate racemization operon protein LarD; Lactic acid channel (characterized)
to candidate GFF2718 Psest_2772 MIP family channel proteins

Query= SwissProt::F9UST3
         (238 letters)



>FitnessBrowser__psRCH2:GFF2718
          Length = 293

 Score =  102 bits (254), Expect = 8e-27
 Identities = 79/244 (32%), Positives = 124/244 (50%), Gaps = 24/244 (9%)

Query: 4   QLIAEFMGTALMIIFGVGVHCSSVLK-GTKYRGSGHIFAITTWGFGISVALFIFGNVC-- 60
           Q IAEF+GTAL+I FG G  C + LK G    G   I  I  WG G+S+A+++   V   
Sbjct: 12  QCIAEFLGTALLIFFGTG--CVAALKLGGAELGLWEISII--WGIGVSMAVYLAAGVSGA 67

Query: 61  -INPAMVLAQCLLGNIAWSLFIPYSVAEVLGGVVGSVIVWIMYADHF-------KASTDE 112
            +NPA+ +A  L G         Y +A+V G    + +V+ +Y+  F       +     
Sbjct: 68  HLNPAVTIALWLFGTFERHRVPAYILAQVAGAFCSAALVYGLYSSLFFDFEQAQQMVRGS 127

Query: 113 ISPITIRNLFCTAP-AVRNLPRNFFVELFDTFIFISGILAISE----IKTPGIVPIGVGL 167
           +  + + ++F T P A  +  + F VE+  T I ++ I+AI++    + +  + P+ +GL
Sbjct: 128 VESLELASIFSTYPHASLSFGQAFLVEMVITAILLAMIMAITDDGNGLPSGPLAPLLIGL 187

Query: 168 LVWAIGMGLGGPTGFAMNLARDMGPRIAHAIL---PIANKADSDWQYGIIVPGIAPFVGA 224
           L+  IG  +G  TGFAMN ARD GP++         +A     D  Y  +VP  AP +GA
Sbjct: 188 LIAVIGGAMGPLTGFAMNPARDFGPKLMTFFAGWGDVAFTGGKDIPY-FLVPIFAPILGA 246

Query: 225 AIAA 228
            + A
Sbjct: 247 CLGA 250


Lambda     K      H
   0.330    0.145    0.470 

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: 263
Number of extensions: 20
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: 238
Length of database: 293
Length adjustment: 25
Effective length of query: 213
Effective length of database: 268
Effective search space:    57084
Effective search space used:    57084
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: 47 (22.7 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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