GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT1 in Desulfoscipio geothermicus DSM 3669

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_900115975.1:WP_092483642.1
          Length = 484

 Score =  246 bits (629), Expect = 1e-69
 Identities = 135/413 (32%), Positives = 221/413 (53%), Gaps = 35/413 (8%)

Query: 18  VVDCSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALAS 77
           + D  + +  L   L   DL ALGVG+ +G G++VL G  A   AGP +V SF+++ +A+
Sbjct: 13  LADKKKNKRGLVPTLGVADLTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAA 72

Query: 78  VLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFD 137
            LA + Y E GA +P  GSAY +SYV++GE+ A++ GWNLIL Y++   +V+  WS+   
Sbjct: 73  TLAAMVYAELGAAIPSAGSAYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMG 132

Query: 138 ELIGKPIGEFSRQHMALNAPGVLAQTP------DIFAVIIIIILTGLLTLGVKESAMVNK 191
           +L+         Q + +  P     +P      ++ A +I++++TGL+  G + S   NK
Sbjct: 133 DLL---------QSVGITLPAAFTSSPFDGGIVNLPAALIVLVITGLIITGTQHSTTANK 183

Query: 192 IFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSG 251
           I     +  +   +  G    +  NW+                      +P+G SGV  G
Sbjct: 184 IIVVAKLAAIALFIALGVQHINPANWRPV--------------------LPYGISGVFHG 223

Query: 252 AATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLD 311
           AA  F+A++GFD +AT  EEVKNPQ+ +P GI+ +L+I  + Y  V+  LT M+ Y  L+
Sbjct: 224 AAIVFFAYIGFDAVATASEEVKNPQRDLPRGIIWTLVISTLLYIVVAGILTGMVKYTNLN 283

Query: 312 IDSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKI 371
             SP+  A    G   A   V++G+L  L++ LL +M+   R+ +AMA D LL      +
Sbjct: 284 TASPVATALLRAGIPWASALVSVGALAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWL 343

Query: 372 NNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424
           + R +TPV  ++  G + A++     +  + +L +IGTL A+  V+   ++LR
Sbjct: 344 HPRLRTPVWDSIIIGVLVALIGAFLPIGLVAELANIGTLTAFIAVSTGAIILR 396



 Score = 57.8 bits (138), Expect = 1e-12
 Identities = 39/116 (33%), Positives = 61/116 (52%), Gaps = 11/116 (9%)

Query: 490 NISAGLLAALIITVCIVAVLGREALAEGTLWA-VFVMTGSVLLCMLVTGIIWRQPESKTK 548
           +I  G+L ALI     + ++  E    GTL A + V TG+++L         R+     +
Sbjct: 354 SIIIGVLVALIGAFLPIGLVA-ELANIGTLTAFIAVSTGAIIL---------RRTNPDLR 403

Query: 549 LSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEA 604
             F++P++P +PVL+I    YL + L   TWVRF  W+ IG  +Y+ YG   S+ A
Sbjct: 404 RPFRLPWMPAIPVLTIISAGYLAINLPPLTWVRFIAWVAIGLVVYWLYGYRKSKLA 459


Lambda     K      H
   0.324    0.138    0.417 

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: 744
Number of extensions: 42
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 484
Length adjustment: 36
Effective length of query: 586
Effective length of database: 448
Effective search space:   262528
Effective search space used:   262528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (25.0 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