Alignments for a candidate for dauA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for dauA in Shewanella loihica PV-4

Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate 5207981 Shew_0497 putative sulfate transporter YchM (RefSeq)

Query= SwissProt::P0AFR2
         (559 letters)



>FitnessBrowser__PV4:5207981
          Length = 565

 Score =  503 bits (1294), Expect = e-146
 Identities = 260/528 (49%), Positives = 378/528 (71%), Gaps = 12/528 (2%)

Query: 32  DLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTAAFVV 91
           +++AG+TVG+IA+PL+MALAI SGV PQ+GLYTA +AGIVIAL GGS+ ++SGPTAAFVV
Sbjct: 21  NILAGLTVGVIALPLSMALAIASGVPPQHGLYTAMIAGIVIALCGGSKVNISGPTAAFVV 80

Query: 92  ILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGIGITIGTMQ 151
           IL P+ QQFGL GLL++ L++G+ L+LMGL + G+LIE +P  VT+GFT+GIG+ I T Q
Sbjct: 81  ILLPIVQQFGLGGLLLSGLMAGVILLLMGLGKLGKLIEIVPYPVTVGFTAGIGVVIATFQ 140

Query: 152 IKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRLGIRLPGHLP 211
           IKDF GL++A   EHYL+K+  +  AL +I+  +  IG +TL +L+ WP+L  ++P HL 
Sbjct: 141 IKDFFGLEVAAGGEHYLEKLSYILQALTSISWQETLIGALTLAVLLAWPKLKSKVPAHLA 200

Query: 212 ALLAGCAVMGIV-NLLGG-HVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSE-- 267
           ALL G  +  ++  ++GG  VATIGS+FHY L DG  G+GIP ++P    PW+LP ++  
Sbjct: 201 ALLVGALIAWVMTQMIGGFSVATIGSRFHYEL-DGLLGSGIPPIMPSFEWPWNLPGADGQ 259

Query: 268 -FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPF 326
              ++++ +R LLP+A ++A+LGA+ESLLCAVV DGM+G KH  N EL+GQGLGNI+ P 
Sbjct: 260 PIGMSFELVRELLPSAITIAILGALESLLCAVVADGMSGKKHNPNDELIGQGLGNILVPL 319

Query: 327 FGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAALLLMV 386
           FGGI ATAAIAR+AANV+AG + P+++V+H + ++  +L+LAPLLS++P+++MAALLL+V
Sbjct: 320 FGGIPATAAIARTAANVKAGGSMPLASVVHGLFILAGILLLAPLLSYIPMASMAALLLVV 379

Query: 387 AWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRIARMT 446
           AWNMSEA   V  L+ AP+DD+++++LC +LTVLFDM IA++VG+ LA++LF+RR   +T
Sbjct: 380 AWNMSEAKHFVRTLKVAPRDDVLILVLCFALTVLFDMTIAVAVGMGLAAMLFIRRSISLT 439

Query: 447 RLAPV-----VVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVILKWDAVPVLD 501
               V       +VP+ V+V  + GPLFF +A      +       R+VIL    V +LD
Sbjct: 440 DARAVETNHQAYEVPESVVVYDINGPLFFGSAHKALKTIALVRPDVRVVILDMSEVTLLD 499

Query: 502 AGGLDAFQRFVKRLP-EGCELRVCNVEFQPLRTMARAGIQPIPGRLAF 548
              + A +   + L  +   L + N++ + L  + RAGI+   G++ +
Sbjct: 500 MSAIVAMESIAQDLSGKQVALIINNLQPRMLLKLRRAGIRKRRGQVEY 547


Lambda     K      H
   0.328    0.142    0.425 

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: 761
Number of extensions: 33
Number of successful extensions: 6
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: 559
Length of database: 565
Length adjustment: 36
Effective length of query: 523
Effective length of database: 529
Effective search space:   276667
Effective search space used:   276667
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: 53 (25.0 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources