Alignments for a candidate for cycA in Thermoactinomyces daqus H-18

GapMind for catabolism of small carbon sources

Alignments for a candidate for cycA in Thermoactinomyces daqus H-18

Align L-alanine and D-alanine permease (characterized)
to candidate WP_160173842.1 JG50_RS0109790 amino acid permease

Query= reanno::WCS417:GFF1065
         (472 letters)



>NCBI__GCF_000763315.1:WP_160173842.1
          Length = 453

 Score =  308 bits (789), Expect = 2e-88
 Identities = 165/444 (37%), Positives = 265/444 (59%), Gaps = 20/444 (4%)

Query: 18  LKRELGERHIRLMALGACIGVGLFLGSAKAIEMAGPAIMLSYIIGGLAILVIMRALGEMA 77
           L+R L ER + ++ LG+ IG GLF+GS+  I  AGP ++ SY++  L +L ++  L  ++
Sbjct: 15  LQRSLSERQMIMIGLGSAIGTGLFMGSSLTIHYAGPGVLFSYLLSSLIVLAMVFCLSRLS 74

Query: 78  VHNPVAGSFSRYAQDYLGPLAGFLTGWNYWFLWLVTCVAEITAVAVYMGVWFPDTPRWIW 137
           V +P AGSF  +A+ YLG   GF   + YW    +    E TA+ +YM  WFP  P WIW
Sbjct: 75  VIHPTAGSFGLHAETYLGSWFGFAVRFTYWAANAIVIGGEATAIGLYMKYWFPGLPSWIW 134

Query: 138 ALAALISMGSINLIAVKAFGEFEFWFALIKIVTIIAMVIGGVGIIAFGFGNDGVALGISN 197
            +A  + +  IN I+V++FG FE+WF+ +K+V +I  ++ G+ +I   FGN         
Sbjct: 135 IIAFSLLIIGINAISVQSFGWFEYWFSTLKVVAVIGFILLGIALI---FGNS--TQSTHY 189

Query: 198 LWAHGGFMPNGVQGVLMSLQMVMFAYLGVEMIGLTAGEAKNPQKTIPSAIGSVFWRILLF 257
           L A+GGF+P+G +GV M   M MF+++G E+I +TAGEAK P++ +  A+  +  R+++F
Sbjct: 190 LLAYGGFLPHGWKGVWMGSAMAMFSFMGTEIIAITAGEAKKPKQALTRAMKWMVARLVIF 249

Query: 258 YVGALFVILSIYPWNEIG---TQGSPFVMTFERLGIKTAAGIINFVVITAALSSCNGGIF 314
           Y+ +  V++ I PWN+IG    Q SPFV   + L I  AAG++NF+++TAALS+ N  ++
Sbjct: 250 YLLSTLVMVCIVPWNQIGGEQIQESPFVKVLQSLHIPYAAGVMNFIILTAALSTMNANLY 309

Query: 315 STGRMLYSLAQNGQAPATFAKTSSNGVPRKALLLSIFALLLGVLLNYLVPEKVFVWVTSI 374
           +  RM++SL+++G APA F K +  G+P  AL++S F L + VLLN   P+  +  +  I
Sbjct: 310 ACTRMMFSLSKSGYAPAVFGKVNRRGIPLMALIVSSFGLGVAVLLNMFDPQ-AYNTLFGI 368

Query: 375 ATFGAIWTWLMILLAQLKFRKSLSPAEQAGLKYRMWLYPVSSYLALAFLLLVVGLMAYFP 434
           + FG I+TW+ I L+  + R+  +            L    + L + FLL ++   A+  
Sbjct: 369 SIFGGIFTWITIFLSYARLRRKKTGKASV-------LAWAGAVLLVLFLLTMLLNQAW-- 419

Query: 435 DTRIALYVGPVFLVLLTVLFYVFK 458
               A+Y G  +L LLT+++   K
Sbjct: 420 --SFAIYTGFCWLFLLTLIYLAKK 441


Lambda     K      H
   0.328    0.142    0.447 

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: 593
Number of extensions: 29
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: 472
Length of database: 453
Length adjustment: 33
Effective length of query: 439
Effective length of database: 420
Effective search space:   184380
Effective search space used:   184380
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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