GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEIIA in Catellicoccus marimammalium M35/04/3

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate WP_083848942.1 C683_RS02545 PTS transporter subunit EIIC

Query= CharProtDB::CH_001857
         (699 letters)



>NCBI__GCF_000313915.1:WP_083848942.1
          Length = 553

 Score =  265 bits (678), Expect = 3e-75
 Identities = 180/567 (31%), Positives = 288/567 (50%), Gaps = 79/567 (13%)

Query: 6   FGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQ 65
           F   QK G+ALM+ +A++PAAG++++IG  +    M QV   ++      + GV E+ G 
Sbjct: 7   FEFWQKFGKALMVVIAVMPAAGLMISIGKLIA---MAQVSLAVT------IGGVTENIGW 57

Query: 66  IVFDNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAV------LLANGTIPSDS 119
            +  NLP+LFA+ +    A        A+ + ++++N    AV      +LAN      +
Sbjct: 58  AIIGNLPILFALAIGGSWAKERAGGAFASGLAFILINRITGAVFGVTKEMLANPEATVHT 117

Query: 120 VERAKFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTI-ELPQYLGFFAGK 178
           +   K     +  + ++L  P L  GVF GII G   A+++N++Y   +LP  L FF GK
Sbjct: 118 IFGQKILVNGY--FTSVLEAPALNMGVFVGIIAGFAGAIIYNKYYNFRKLPNCLSFFNGK 175

Query: 179 RFVPIVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEAN---PTLAAFIFGVIERSLIP 235
           RFVP V  + ++I+ L++ V WP  Q G+N F   + ++    P  A FI+G +ER L+P
Sbjct: 176 RFVPFVVILWSVIIALLLSVFWPFAQTGINEFGKWIAQSGDSAPFWAPFIYGTLERLLLP 235

Query: 236 FGLHHIFYSPFWYEFFSYK------SAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYP 289
           FGLHH+   P  Y            + AG+ + G   +++A + D + L     MT  + 
Sbjct: 236 FGLHHMLTIPMNYTDLGGTYHILTGAQAGQAVLGQDPLWLAWVTDLINLKEKGDMTQYHQ 295

Query: 290 FM------------MFG----LPAAALAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEP 333
            +            M G    L     A+Y   +P+ KK+   I  SAAL  FLTG+TEP
Sbjct: 296 LLESIRPARFKVGQMIGSSGILMGVTFAMYRNVEPKRKKVYKQIFLSAALAVFLTGVTEP 355

Query: 334 LEFSFLFVAPVLFAIHCLFAGLSFMVMQLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLV 393
           LEF F+F    L+ ++ L  G++F +  ++++++             FG +   T   + 
Sbjct: 356 LEFMFMFAGIPLYVVYALLQGVAFGLADIIDLRL-----------HAFGNIELLTRLPMS 404

Query: 394 IPVGLGLAVI------------YYFGFRFAIRKFNLKTPGR----------EDAAEETAA 431
           I  GLG+ +I             YF   F I+KF++ TPGR            A++ T A
Sbjct: 405 IKAGLGMDIINFIITCIVFFFLAYFVANFMIKKFHIATPGRLGNYIEGNDDSSASDTTTA 464

Query: 432 PGKT--GEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKV-DKDRLKQLGASGV 488
              T   EA +    I+Q +G +ENI  +DAC+TRLRVTV D  KV D++  K+ GA G+
Sbjct: 465 TSSTKPSEANNQVMNIIQLLGGKENIVDVDACMTRLRVTVKDTTKVADEEAWKKEGAMGL 524

Query: 489 LEVGNNIQAIFGPRSDGLKTQMQDIIA 515
           +   N +QA++GP++D LK+ + D ++
Sbjct: 525 IHKNNGVQAVYGPKADVLKSDINDYLS 551


Lambda     K      H
   0.323    0.141    0.412 

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: 913
Number of extensions: 64
Number of successful extensions: 10
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: 699
Length of database: 553
Length adjustment: 37
Effective length of query: 662
Effective length of database: 516
Effective search space:   341592
Effective search space used:   341592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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