GapMind for catabolism of small carbon sources

 

Alignments for a candidate for CAT1 in Caulobacter crescentus NA1000

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate CCNA_00435 CCNA_00435 amino acid transporter

Query= CharProtDB::CH_091324
         (622 letters)



>FitnessBrowser__Caulo:CCNA_00435
          Length = 483

 Score =  233 bits (593), Expect = 2e-65
 Identities = 154/425 (36%), Positives = 230/425 (54%), Gaps = 20/425 (4%)

Query: 15  RRKVVDC----SREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISF 70
           RRK +D       +  +L + L+   LVALGVG+ +G G+Y L G V    AGP +++SF
Sbjct: 13  RRKAIDTITAGHADSHQLKKTLSWPHLVALGVGAIVGTGIYTLTG-VGAGLAGPGVILSF 71

Query: 71  LIAALASVLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVAR 130
           LIA      A LCY E    +P +GSAY YSY  +GE  A+  GW+LIL Y +  ++VA 
Sbjct: 72  LIAGAVCACAALCYAELSTMIPASGSAYTYSYAAMGEPVAWFVGWSLILEYTLVCAAVAV 131

Query: 131 AWSATFDELIGKPIGEFSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAMVN 190
            WSA    L  K IG F    +A    G L   P   AV I + + GLL LG +ESA VN
Sbjct: 132 GWSAHAHGLF-KMIG-FPDALLAGPHQGGLINMP---AVFISMAVAGLLALGTRESATVN 186

Query: 191 KIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLS 250
            +   + ++ L   VV      ++ ++      F  N    +V   EG        GV++
Sbjct: 187 MVLVFVKIIALIVFVVLCLPAFNLAHFT----PFMPNGFQAHVP--EGAAADAAKVGVMA 240

Query: 251 GAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCL 310
            A+  F+AF GFD ++T  EE KNP++ + +GIV S+ +C   Y  + AA+++      +
Sbjct: 241 AASLIFFAFYGFDAVSTAAEETKNPKRDLTIGIVGSMAVCTAIYM-IVAAVSIGASRTEV 299

Query: 311 DIDSPLPGAFKHQGWEEAKYA--VAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFL 368
              S  P  F  +     K A  VA+ ++ AL T +L  M+   R+ + MA DGLL + L
Sbjct: 300 FSKSEAPLVFILESLNHGKIAQLVALAAVIALPTVILAFMYGQSRIFFVMARDGLLPRAL 359

Query: 369 AKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRY-QP 427
           +K+N +T TPV+ T+ +G +AAV++ L  LKD+ +L + GTL A+  V A V++LR  +P
Sbjct: 360 SKVNAKTGTPVMMTLLTGVLAAVISGLLSLKDIAELANAGTLWAFIAVGASVILLRLREP 419

Query: 428 EQPNL 432
            +P +
Sbjct: 420 NRPRV 424


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: 725
Number of extensions: 43
Number of successful extensions: 9
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: 483
Length adjustment: 36
Effective length of query: 586
Effective length of database: 447
Effective search space:   261942
Effective search space used:   261942
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 Sep 17 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