GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cycA in Corynebacterium deserti GIMN1.010

Align L-alanine and D-alanine permease (characterized)
to candidate WP_053545852.1 CDES_RS12695 amino acid permease

Query= reanno::pseudo5_N2C3_1:AO356_17670
         (473 letters)



>NCBI__GCF_001277995.1:WP_053545852.1
          Length = 499

 Score =  349 bits (896), Expect = e-100
 Identities = 184/448 (41%), Positives = 271/448 (60%), Gaps = 8/448 (1%)

Query: 12  TAQGGPLKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMR 71
           TA      + L  R + ++A+G  IG GLF+G+   +  AGP I++SY I G+   +I+R
Sbjct: 24  TAGDNDYHKGLSTRQVNMIAIGGAIGTGLFMGAGGRLAQAGPGIVISYAICGVLAFLILR 83

Query: 72  ALGEMAVHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGI---- 127
           ALGE+ ++ P +GSF  YA+++ G  A F TGW YW  W +T + +ITA A+YM      
Sbjct: 84  ALGELVMYRPSSGSFVSYAREFYGEKAAFATGWLYWLNWSMTAIVDITAAALYMNFFGRY 143

Query: 128 --WFPDVPRWIWALAALVSMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFG 185
             W   VP+WIWALAAL+ +  +NLI+VK FGE EFWFALIK+V + A ++ G   + FG
Sbjct: 144 VPWISAVPQWIWALAALLLVLGMNLISVKVFGELEFWFALIKVVALTAFLVVGTYFVIFG 203

Query: 186 FGNDGVALGISNLWAHGGFMPNGVSGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPN 245
              +G   G S +  +GG +PNG+  VL+ +Q V+FAY  +E++G  AGE +NP+K +P 
Sbjct: 204 TPIEGHTTGWSIIQDNGGILPNGILPVLVLMQGVVFAYASIELLGTAAGEVENPEKVMPK 263

Query: 246 AIGSVFWRILLFYVGALFVILSIYPWNEIGTQGSPFVMTFERLGIKTAAGIINFVVITAA 305
           AI +V +RI +FYVG+L ++  + P+       SPFV  F  +GI     I+N VV+TAA
Sbjct: 264 AINTVIFRIAVFYVGSLVLLSLLLPYTAYKAGESPFVTFFSAIGIPGMDVIMNLVVLTAA 323

Query: 306 LSSCNGGIFSTGRMLYSLAQNGQAPAGFAKTSTNGVPRRALLLSIAALLLGVLLNYLVPE 365
           +SS N G++STGR+L S++ NG AP    + S +GVP   +L++ A   LGV LN LVP 
Sbjct: 324 MSSLNAGLYSTGRILRSMSLNGSAPKFAGRISASGVPYGGILITAAIAALGVGLNALVPA 383

Query: 366 KVFVWVTSIATFGAIWTWVMILLAQLKFRKSLSASERAALKYRMWLYPVSSYLALAFLVL 425
           + F  V + A  G I +W MI+L  +   K  +  E     +RM   P +S++ L  LVL
Sbjct: 384 QAFEIVLNFAAIGIIASWGMIVLCHIALVKKSTRGELTRPSFRMPFAPYTSWIVLVALVL 443

Query: 426 VVGLMAYFPDTRVALYVGPAFLVLLTVL 453
           +V LMA+  D+ V  +      V++ +L
Sbjct: 444 IVILMAF--DSPVGTWTVAGLAVIIPLL 469


Lambda     K      H
   0.328    0.142    0.444 

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: 626
Number of extensions: 30
Number of successful extensions: 2
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: 473
Length of database: 499
Length adjustment: 34
Effective length of query: 439
Effective length of database: 465
Effective search space:   204135
Effective search space used:   204135
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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