GapMind for catabolism of small carbon sources

 

Alignments for a candidate for alsT in Desulfovibrio vulgaris Hildenborough

Align Sodium/alanine symporter AgcS; Alanine permease (characterized)
to candidate 206150 DVU0724 sodium/alanine symporter family protein

Query= SwissProt::Q6LX42
         (453 letters)



>MicrobesOnline__882:206150
          Length = 468

 Score =  462 bits (1190), Expect = e-135
 Identities = 244/451 (54%), Positives = 310/451 (68%), Gaps = 14/451 (3%)

Query: 1   MDFVSLVNTVNSFVWGPYMLVLLLGTGIFLTLRLGFMQIHTLPYALKLAFSKHQDETSEG 60
           M  + L  +VN+FVWGP +L LL+GTGI+LT+RLG +Q+  LP AL+  F +  +   EG
Sbjct: 1   MTTLQLFESVNAFVWGPPLLALLVGTGIYLTIRLGLLQVVRLPLALRYVFGRDDEHHEEG 60

Query: 61  DISHFQALMTALAATIGTGNIAGVATAYVLGGPGAIFWMWVTAFFGMATKYAEAVLAIKY 120
           D+S F AL TALAATIGTGNI GVATA   GGPGA+FWMWV AFFGMATKYAE +LA+KY
Sbjct: 61  DVSSFAALCTALAATIGTGNIVGVATAVAAGGPGALFWMWVAAFFGMATKYAEGLLAVKY 120

Query: 121 RTVDDNGEMAGGPMYFLEKGLPDHGLGKILGVAFAFFGAFAA-FGIGNMVQTNSVADAVA 179
           R  D NG+M+GGPMY+LE+GL      ++L  AFA  G   A FGIG   Q N++ DA +
Sbjct: 121 RVTDANGQMSGGPMYYLERGLG----SRMLARAFALCGILVAFFGIGTFAQVNAIKDAAS 176

Query: 180 SNFGVDPLITGFVLAIFTAAVILGGIKSIGKATGIIVPFMAVFYILAGLVILAMNIGYII 239
            + G+ PL T  VL    A V LGG++SI +    +VPFMAVFYI+A   +L M++  I 
Sbjct: 177 LSLGIPPLATAVVLTTTVALVTLGGLRSIARVAEKVVPFMAVFYIIASCAVLVMHLDRIP 236

Query: 240 PAFGTIFSSAFNFSAGFGALIG----TAIMWGVKRGVFSNEAGLGSAPIAAAAAKTDHPG 295
            A   I  SAFN  A  G   G    TA+  GV RGVFSNE+GLGSAPIAAAAA+T    
Sbjct: 237 DAVMVILHSAFNPQAALGGAAGMTVLTAMRAGVARGVFSNESGLGSAPIAAAAARTKSCV 296

Query: 296 RQALVSMTGTFLDTIVVCTITGLVLTIAGLKAFPGLTDLTGASLTAASFDALM--PMGGL 353
           RQ L+SMTGTF DTIV+CT+TGLVL + G+   P    L GA++T A+F A +   +G  
Sbjct: 297 RQGLISMTGTFFDTIVICTMTGLVLVVTGVWNDP---QLAGAAMTNAAFAAGLESSLGQY 353

Query: 354 IVTIGLVFFAYSTVLGWSYYGEKCFEYLIGTKGIRLYRIAFVLVAFWGATASLPLVWNIA 413
             T+GL+ FA++T+LGW+YYGE+C EYL G +GI  YR+ F+ +   GA   L L+W +A
Sbjct: 354 AATLGLILFAFTTILGWNYYGERCTEYLFGVRGILPYRLVFIGLVAAGAFVHLELIWVLA 413

Query: 414 DTLNGAMAIPNLIGLLLLSGVVVSETKAFNE 444
           D +NG MAIPNLIGLL LSGV+++ET+AF E
Sbjct: 414 DIVNGLMAIPNLIGLLGLSGVIIAETRAFFE 444


Lambda     K      H
   0.326    0.141    0.424 

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: 661
Number of extensions: 39
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: 453
Length of database: 468
Length adjustment: 33
Effective length of query: 420
Effective length of database: 435
Effective search space:   182700
Effective search space used:   182700
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 (21.6 bits)
S2: 51 (24.3 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