GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Herbaspirillum seropedicae SmR1

Align Organic acid uptake porter, DctA of 444 aas and 8 - 10 putative TMSs (characterized)
to candidate HSERO_RS19090 HSERO_RS19090 C4-dicarboxylate ABC transporter

Query= TCDB::Q848I3
         (444 letters)



>FitnessBrowser__HerbieS:HSERO_RS19090
          Length = 431

 Score =  284 bits (726), Expect = 4e-81
 Identities = 173/418 (41%), Positives = 249/418 (59%), Gaps = 27/418 (6%)

Query: 15  VIVAIAIGILLGH--FYPQTGVALKPLG-------DGFIKLIKMVIAPIIFCTVVSGIAG 65
           +  A+ +GIL+G+  F        K L        D F++LIKMVIAP++F T+V GIA 
Sbjct: 11  IFAAMLLGILVGYLIFSHNDKAQAKELAGYISIASDLFLRLIKMVIAPLVFSTLVVGIAH 70

Query: 66  MQNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGNGMHIDVSTLDASKVAAYVTA 125
           M + KSVG+  G +L +F I S ++L +G+++ N++QPG G+      L +   A    A
Sbjct: 71  MGDAKSVGRIFGKSLAWFFIASLVSLALGMIMANLLQPGAGV-----ALPSPDAAGAGLA 125

Query: 126 GKDQSIVGFILNVIPNTIVGAFANGDILQVLMFSVIFGFALHRLGAYGKPVLDFIDRFAH 185
               ++  F  +++P +IV A A  ++LQV++FS+ FG AL  LG  GK +L  ID  +H
Sbjct: 126 TSKFTVKEFFNHLVPKSIVEAMAQNEVLQVVVFSMFFGIALASLGERGKHLLAVIDDLSH 185

Query: 186 VMFNIINMIMKLAPIGALGAMAFTIGAYGVGSLVQLGQLMICFYITCVLFVLVVLGAICR 245
            M  I   +MK AP+    AMA T+   G+  LV     M  FY     F LV+L  I  
Sbjct: 186 TMLKITVYVMKFAPVAVFAAMAATVAVNGLEILVSFAVFMRDFY-----FSLVLLWVILI 240

Query: 246 AHGFSVLK-----LIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGY 300
           A GF  LK     L+  I+E  L+   T+SSE+A P++L  ++R G K+ +   V+P GY
Sbjct: 241 AVGFIFLKKRIFHLLALIKEAFLLAFATASSEAAYPKLLDALDRFGVKRKISSFVMPMGY 300

Query: 301 SFNLDGTSIYLTMAAVFIAQATDTHMDITHQITLLLVLLLSSKGAAGVTGSGFIVLAATL 360
           SFNLDG+ IY T A +FIAQA   HM I+ QIT++LVL+L+SKG AGV  +  +V+AATL
Sbjct: 301 SFNLDGSMIYCTFATLFIAQAYGIHMPISTQITMMLVLMLTSKGIAGVPRASLVVIAATL 360

Query: 361 SAVGHLPVAGLALILGIDRFMSEARALTNLVGNAVATVVVAKWVKEL--DEDQLQAEL 416
               ++P AGL +ILGID F+   R+ TN VGN++A+ VVAKW   L  +E+  +AE+
Sbjct: 361 HQF-NIPEAGLLVILGIDTFLDMGRSATNAVGNSIASAVVAKWEGGLMTEEEAARAEV 417


Lambda     K      H
   0.326    0.142    0.402 

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: 450
Number of extensions: 23
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: 444
Length of database: 431
Length adjustment: 32
Effective length of query: 412
Effective length of database: 399
Effective search space:   164388
Effective search space used:   164388
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.

Links

Downloads

Related tools

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