GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT in Methylocystis bryophila S285

Align Plastidic cationic amino acid transporter, CAT, of 582 aas and 14 TMSs (characterized)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease

Query= TCDB::ALD51314.1
         (582 letters)



>NCBI__GCF_002117405.1:WP_102938052.1
          Length = 481

 Score =  248 bits (633), Expect = 4e-70
 Identities = 151/466 (32%), Positives = 241/466 (51%), Gaps = 31/466 (6%)

Query: 50  MKRSLRWYDLVGFGVGGMVGAGVFVTSGRASSHCAGPAVVLSYAIAGFCALLSAFCYTEF 109
           +KR+L W  L+  G+GG++GAG+FV +G+A++  AGP V +S+ ++G      A CY E 
Sbjct: 29  LKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLACTFVALCYAEL 88

Query: 110 AVDMPVAGGAFSYIRITFGEFLAFLTGANLIIDYVLSNAAVARSFTGY---LCTALGIES 166
           A  +P AG  ++Y  +T GE  A++ G NL+++Y    A VA  + GY   +   LGI  
Sbjct: 89  AALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFNRVMQGLGIHL 148

Query: 167 KLRIT---------VNGLPDGFNEIDVVAVLVVLALTVIICYSTRESSVLNMVLTVLHIV 217
              +T         + G    FN   V A  ++L LT ++   T ESS  N ++ V+ ++
Sbjct: 149 PEALTSAYFANAHSIGGTHGVFN---VPAAAIILLLTALLMRGTSESSFFNNIIVVIKVM 205

Query: 218 FIVFVIVIGFTRGDTKNFTKAGDSNHASGFFPFGASGVFNGAAMVYLSYIGYDAVSTMAE 277
            ++ VI +G    D  N+T     N    F  FG SGV  GA++V+ +YIG+D VST A+
Sbjct: 206 VVLVVIFVGAAHVDAANWTPLIPEN-TDHFGHFGWSGVVRGASVVFFAYIGFDGVSTAAQ 264

Query: 278 EVKNPVKDIPVGVSGSVILVTVLYCLMAASMSMLLPYDMIDPDAPFSGAFMGSDGWRWVS 337
           E   P +D+P+G+ GS+++ T+LY  +AA  + ++ Y  +    P +   M   G  W+S
Sbjct: 265 EAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYKELGVPDPMA-LVMDRTGVAWLS 323

Query: 338 NVIGVGAGFGILTSLLVAMLGQARYMCVIGRSSVVPAWFAKVHPKTSTPVNASAFLGICT 397
            V+ +GA  G+ T++L+ + GQ R    + +  ++P  FA VHP   TP  + A +G+  
Sbjct: 324 WVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVFAAVHPVWRTPAVSQALVGVFV 383

Query: 398 AAIALFTDLQILLNLVSIGTLFVFYMVANAVIYKRYVSVGVTNPW-----PTLSYLFCFS 452
           A  A    + IL  +VSIGTL  F +V  AV++ R     +  P+     P +  L   S
Sbjct: 384 ALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLRRSQPDMHRPFRAPGIPAMPLLGIAS 443

Query: 453 LTSILFTLLWQFAPPGKPKAFMLGACTAIAIGVLQLFHYMVPQARK 498
             +++  L         P    L      AIG+   F Y V  A++
Sbjct: 444 CLALMVAL---------PLETWLRLIVWTAIGMAIYFFYGVKHAKR 480


Lambda     K      H
   0.326    0.139    0.423 

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: 660
Number of extensions: 36
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: 582
Length of database: 481
Length adjustment: 35
Effective length of query: 547
Effective length of database: 446
Effective search space:   243962
Effective search space used:   243962
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 Apr 09 2024. 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