GapMind for catabolism of small carbon sources

 

Alignments for a candidate for larD in Pedobacter sp. GW460-11-11-14-LB5

Align Glycerol uptake facilitator protein 4; D/L-lactic acid transporter; Lactic acid channel (characterized)
to candidate CA265_RS07865 CA265_RS07865 aquaporin

Query= SwissProt::F9UMX3
         (238 letters)



>FitnessBrowser__Pedo557:CA265_RS07865
          Length = 246

 Score =  168 bits (425), Expect = 1e-46
 Identities = 96/242 (39%), Positives = 135/242 (55%), Gaps = 25/242 (10%)

Query: 6   LAEFMGTALMIIFGVGVHCSEVLKGTKYRGSGHIFAITTWGFGITIALFIFG---NVCIN 62
           LAEF+GTALMI+ G GV  + VLKGTK   SG I   T W   + + + + G      +N
Sbjct: 5   LAEFIGTALMILLGNGVVANVVLKGTKGNNSGWIVITTAWALAVFVGVVVAGPYSGAHLN 64

Query: 63  PAMVLAQCILGNLSWSLFIPYSVAEVLGGVVGAVIVWIMYADHFAASADE---ISPITIR 119
           P + L   I    SW+L   Y +A++ G + G+ +VW++Y DHF A+ D+    +P    
Sbjct: 65  PIVTLGLAIGKGFSWALAPFYIIAQLAGAMTGSFLVWLIYKDHFDATDDQGLKAAP---- 120

Query: 120 NLFSTAPAVRNLPRNFFVEFFDTFIFISGILAISEV----KTPGIVPIGVG--------L 167
             F+TAPA+RN+  N   E   TF+ I  I   ++     K     PIG+G         
Sbjct: 121 --FATAPAIRNISSNLLSEIIGTFVLIFVIFYFTDASMGTKETVTTPIGLGSMGAIPVAF 178

Query: 168 LVWAIGMGLGGPTGFAMNLARDMGPRIAHAILPIKNKADSDWQYGIIVPGIAPFVGAACA 227
           LVW IG+ LGG TG+A+N ARD+GPRI H ++P+K K  SDW Y   VP + P +G+  A
Sbjct: 179 LVWVIGLALGGTTGYAINPARDLGPRIIHFLIPMKGKGGSDWSYA-WVPIVGPIIGSVLA 237

Query: 228 AL 229
           A+
Sbjct: 238 AV 239


Lambda     K      H
   0.330    0.146    0.468 

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: 223
Number of extensions: 13
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: 238
Length of database: 246
Length adjustment: 23
Effective length of query: 215
Effective length of database: 223
Effective search space:    47945
Effective search space used:    47945
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: 46 (22.3 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