GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glt in Paraburkholderia bryophila 376MFSha3.1

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate H281DRAFT_03336 H281DRAFT_03336 Na+/H+-dicarboxylate symporter

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Burk376:H281DRAFT_03336
          Length = 438

 Score =  428 bits (1100), Expect = e-124
 Identities = 207/412 (50%), Positives = 299/412 (72%)

Query: 7   KSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAGMES 66
           +SLY QVL  + +G+ +GHF P+ G  +KP  D FV L++M+IAP++FCT+V+GI  + S
Sbjct: 8   RSLYVQVLLGMVLGVAVGHFLPQAGALLKPFSDAFVGLVRMMIAPIVFCTIVSGITSLAS 67

Query: 67  MKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQAKD 126
            KA+GRT   AL  F +++ +AL  GL+   V++PGAGM++D   LD   +A Y   A+ 
Sbjct: 68  GKAIGRTIFKALALFYLLTVVALAFGLVTAIVLRPGAGMHIDAHGLDTSILAQYVKHAQP 127

Query: 127 QGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFSQVIF 186
            G+VAF + VIP +++GAF  G++L VLL ++LFGF+L+     G+ +  +I+  + V+F
Sbjct: 128 GGLVAFALSVIPETMLGAFEKGDVLPVLLLSLLFGFSLNSCPKAGRPVLALIDGVAHVLF 187

Query: 187 GIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIAKATG 246
            I+ MIMRLAP+GAFGAMAFT+G++G+ ++  LG L++CFY+ C+LF+ LVL S+A+  G
Sbjct: 188 RILAMIMRLAPLGAFGAMAFTVGRFGIRSVGSLGMLMVCFYVACLLFIALVLASLARLHG 247

Query: 247 FSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNLDGTS 306
           F++++ +RY+REELLIVL TSS+E  LPR++ K+E LGC K VVGLV+P GYSFNLDGT+
Sbjct: 248 FALWRLLRYMREELLIVLATSSTEPVLPRLIVKLEALGCDKGVVGLVLPAGYSFNLDGTA 307

Query: 307 IYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVGHLPV 366
           IYLT+A++FIAQA +  +       +L V+LL+SKGAAGV+GSG + L ATL+ +  LPV
Sbjct: 308 IYLTLASMFIAQACDVPLSASQIAMMLAVMLLTSKGAAGVSGSGLVALVATLTVIPDLPV 367

Query: 367 AGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRA 418
           AG+AL++GIDRFMSEARALT+++ N  A I V+ W    D  +L  +L   A
Sbjct: 368 AGVALLVGIDRFMSEARALTSVISNACAVIFVSMWEGACDRARLAQMLGAAA 419


Lambda     K      H
   0.327    0.142    0.401 

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: 539
Number of extensions: 25
Number of successful extensions: 1
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: 428
Length of database: 438
Length adjustment: 32
Effective length of query: 396
Effective length of database: 406
Effective search space:   160776
Effective search space used:   160776
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: 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