GapMind for catabolism of small carbon sources

 

Aligments for a candidate for metP in Desulfovibrio vulgaris Miyazaki F

Align Transporter, component of The methionine/alanine uptake porter, MetPS (Trotschel et al., 2008) (MetP is the transporter; MetS is an essential auxiliary subunit) (characterized)
to candidate 8500111 DvMF_0874 sodium:neurotransmitter symporter (RefSeq)

Query= TCDB::Q8NRL8
         (579 letters)



>lcl|FitnessBrowser__Miya:8500111 DvMF_0874 sodium:neurotransmitter
           symporter (RefSeq)
          Length = 454

 Score =  192 bits (487), Expect = 3e-53
 Identities = 128/414 (30%), Positives = 210/414 (50%), Gaps = 27/414 (6%)

Query: 34  REVFSSRSVFILAAIGSAVGLGNIWRFPYVAYDNGGGAFLIPYAIALLTAGIPLLFLDFA 93
           R+ F++R   + A +GSAVGLGNIW+FP +   NGG +FL+ Y +A L  G+P++  +  
Sbjct: 9   RDGFATRLGVLAATLGSAVGLGNIWKFPALTGQNGGASFLLVYVLATLLVGLPVMISEIM 68

Query: 94  IGHRYRGSAPLAFRRFKKQTE---TIGWIQVGIAFFITIYYAAIIGWAGLYAFKSLNKAW 150
           +G R R +A   FR+   + +    +G+  V  AF I  +Y  + GW   Y FKSL+   
Sbjct: 69  LGRRARANAVGTFRQLAPKGQPWHLVGFSGVVAAFLIMGFYTDVAGWVFAYIFKSLSGEI 128

Query: 151 GADPDTYFFSDFLNFDSEAVVSMDIVPQIAIALFIVWIAAIVVLAIGVDKGIGRVSMVFM 210
                      F     EA+V  D V  +     ++ + +++++A GV +GI R + V M
Sbjct: 129 ATTDPAVAAKAF-----EALVG-DPVQSLLWQWGVLVLISVIIIA-GVAQGIERTTKVLM 181

Query: 211 PLLVIIFLIVVIQAVLLPGAEIGLDALFTPNWEALKNPTVWIAAYGQIFFSLSVGFGIML 270
           P+L+++ + V  +++ LP A  GL  LFTP++  +  P V + A G  FF LS+G G M 
Sbjct: 182 PVLLLLLVAVCARSLTLPKAAEGLAFLFTPDFSKI-TPGVILMALGLAFFKLSIGMGTMT 240

Query: 271 TYSSYLKPRTNLTSTGLVTGFANSSFEVLAGIGVFAALGFMAANAGVGVDEVATSGIGLA 330
           TY SY +   ++  T       + +  +LAG+ VF A+     N G       ++G  L 
Sbjct: 241 TYGSYFRNDQDIPLTATRVMLCDLTISILAGMAVFPAV----FNFGF----EPSAGPSLL 292

Query: 331 FVAFPAIINEMPLGGLFGFLFFSSLTIAGFTSLFSLLEVVVSAVKDKFGLNRKATAIGVG 390
           F+  PA+   +P G +F  +FF    IA   ++ SLLEV V+ + + FG+ RK   I   
Sbjct: 293 FMTIPAVFTSLPGGQVFMVIFFCLTAIAATGAMLSLLEVPVAWLAESFGMPRKRATILTS 352

Query: 391 VVMALLSLGLFSTTS--------GLATLDIMDKFTNNIGIVAVALIAVVSIDWV 436
           V +A++ L    + S        G+   D+ D  ++N+ +    +   +   WV
Sbjct: 353 VTLAIIGLPATLSMSTMANVKIFGMTVFDLYDFLSSNVLLPVGGIFICLFAGWV 406


Lambda     K      H
   0.325    0.141    0.430 

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: 580
Number of extensions: 30
Number of successful extensions: 5
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: 579
Length of database: 454
Length adjustment: 35
Effective length of query: 544
Effective length of database: 419
Effective search space:   227936
Effective search space used:   227936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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