GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgl in Pseudomonas fluorescens GW456-L13

Align β-glucosidase (BglX;STM2166) (EC 3.2.1.21) (characterized)
to candidate PfGW456L13_4567 Periplasmic beta-glucosidase (EC 3.2.1.21)

Query= CAZy::AAL21070.1
         (765 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4567
          Length = 763

 Score =  967 bits (2499), Expect = 0.0
 Identities = 481/768 (62%), Positives = 599/768 (77%), Gaps = 8/768 (1%)

Query: 1   MKWLCSVGVAVSLAMQPALAENLFGNHPLTPEARDAFVTDLLKKMTVDEKIGQLRLISVG 60
           MK LC +G+ VSLA    LA       P   E ++AFV++L+K+MT+DEKIGQLRLIS+G
Sbjct: 1   MKKLCLLGLFVSLASHNVLAATT----PAPLENKEAFVSNLMKQMTLDEKIGQLRLISIG 56

Query: 61  PDNPKEAIREMIKDGQVGAIFNTVTRQDIRQMQDQVMALSRLKIPLFFAYDVVHGQRTVF 120
           P+ P+E IR+ I  G +G  FN++TR + R MQD  M  SRLKIP+FFAYDV+HG RT+F
Sbjct: 57  PEMPREMIRKEIAAGNIGGTFNSITRPENRPMQDAAMR-SRLKIPMFFAYDVIHGHRTIF 115

Query: 121 PISLGLASSFNLDAVRTVGRVSAYEAADDGLNMTWAPMVDVSRDPRWGRASEGFGEDTYL 180
           PI L LASS+++DA+   GR++A EAA D L++T+APMVD+SRDPRWGR SEGFGEDTYL
Sbjct: 116 PIPLALASSWDMDAIGLSGRIAAKEAAADSLDITFAPMVDISRDPRWGRTSEGFGEDTYL 175

Query: 181 TSIMGETMVKAMQGKSPADRYSVMTSVKHFAAYGAVEGGKEYNTVDMSSQRLFNDYMPPY 240
            S +   MVKA QG       S+M SVKHFA YGAVEGG++YN VDMS  +++ DY+PPY
Sbjct: 176 VSRIAGVMVKAFQGTGANAADSIMASVKHFALYGAVEGGRDYNVVDMSPVKMYQDYLPPY 235

Query: 241 KAGLDAGSGAVMVALNSLNGTPATSDSWLLKDVLRDEWGFKGITVSDHGAIKELIKHGTA 300
           +A +DAG+G VMVALNS+NG PAT+++WL+ D+LR EWGFKG+ VSDHGAI ELIKHG A
Sbjct: 236 RAAIDAGAGGVMVALNSINGVPATANTWLMNDLLRKEWGFKGLAVSDHGAIFELIKHGVA 295

Query: 301 ADPEDAVRVALKAGVDMSMADEYYSKYLPGLIKSGKVTMAELDDATRHVLNVKYDMGLFN 360
           AD  +A ++A+KAG+ MSM D  Y K LPGL+KSG++  +++D+A R VL  KYDMGLF 
Sbjct: 296 ADGREAAKLAIKAGIHMSMNDTLYGKELPGLLKSGEIQQSDIDNAVRAVLGAKYDMGLFK 355

Query: 361 DPYSHLGPKESDPVDTNAESRLHRKEAREVARESVVLLKNRLETLPLKKSGTIAVVGPLA 420
           DPY  +G  E DPVDT A+SRLHR EAR+VAR S VLLKNR +TLPLKK+  IA+VGPLA
Sbjct: 356 DPYLRIGKAEDDPVDTYADSRLHRAEARDVARRSQVLLKNRNDTLPLKKTAKIALVGPLA 415

Query: 421 DSQRDVMGSWSAAGVANQSVTVLAGIQNAVGDGAKILYAKGANITNDK---GIVDFLNLY 477
            +  D+MGSW+AAG   QSVT+  G+ NA+GD + ++YA+GANIT+D    G ++FLN  
Sbjct: 416 KAPIDMMGSWAAAGRPAQSVTLFDGMTNALGDKSTLIYARGANITSDPKILGYLNFLNFD 475

Query: 478 EEAVKIDPRSPQAMIDEAVQAAKQADVVVAVVGESQGMAHEASSRTNITIPQSQRDLITA 537
              V  DPR    +IDEAV+AAK ADVVVA VGES+GM+HE+SSRT++ IP++QR+LI A
Sbjct: 476 APEVVDDPRPANVLIDEAVKAAKDADVVVAAVGESRGMSHESSSRTDLNIPENQRELIRA 535

Query: 538 LKATGKPLVLVLMNGRPLALVKEDQQADAILETWFAGTEGGNAIADVLFGDYNPSGKLPI 597
           LKATGKPLVLVLMNGRPL +++E +QADAILETWF+GTEGGNAIADVLFGDYNPSGKLPI
Sbjct: 536 LKATGKPLVLVLMNGRPLTILEEKEQADAILETWFSGTEGGNAIADVLFGDYNPSGKLPI 595

Query: 598 SFPRSVGQIPVYYSHLNTGRPYNPEKPNKYTSRYFDEANGPLYPFGYGLSYTTFTVSDVT 657
           S PRSVGQIP YY+HL  GRP+ P KP  YTS+YFD+  GPLYPFGYGLSYT F++SD+ 
Sbjct: 596 SIPRSVGQIPTYYNHLTIGRPFTPGKPGNYTSQYFDDTTGPLYPFGYGLSYTEFSLSDMA 655

Query: 658 LSSPTMQRDGKVTASVEVTNTGKREGATVIQMYLQDVTASMSRPVKQLKGFEKITLKPGE 717
           LSS T+ + GK+ ASV V NTGKR+G TV+Q+Y+QD T SM RP+K+LK F+K+ +K GE
Sbjct: 656 LSSTTLNKTGKLDASVTVKNTGKRDGETVVQLYIQDETGSMIRPIKELKNFQKVMIKAGE 715

Query: 718 RKTVSFPIDIEALKFWNQQMKYDAEPGKFNVFIGVDSARVKQGSFELL 765
           +K V F I  + LKF+N Q+KY AEPGKFNV IG+DS  V Q SFELL
Sbjct: 716 QKVVHFTITEDDLKFYNTQLKYAAEPGKFNVQIGLDSEDVTQQSFELL 763


Lambda     K      H
   0.316    0.132    0.380 

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: 1568
Number of extensions: 58
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: 765
Length of database: 763
Length adjustment: 40
Effective length of query: 725
Effective length of database: 723
Effective search space:   524175
Effective search space used:   524175
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 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