Alignments for a candidate for bgl in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Klebsiella michiganensis M5al

Align β-glucosidase (BglA49) (EC 3.2.1.21) (characterized)
to candidate BWI76_RS11890 BWI76_RS11890 glycosyl hydrolase

Query= CAZy::ADK91094.1
         (790 letters)



>FitnessBrowser__Koxy:BWI76_RS11890
          Length = 785

 Score =  730 bits (1885), Expect = 0.0
 Identities = 383/782 (48%), Positives = 508/782 (64%), Gaps = 21/782 (2%)

Query: 10  EFTTLAHSMTPAELADILNGHGMWKTAQNERLGIPNIVMTDGTYGVRYSIQQIDHDEKGG 69
           +F T   +M+  E   +L G G+W+TA   + GI +I+MTDGTYGVRYS  QID  EK  
Sbjct: 4   DFNTTLAAMSAEEKVALLTGSGLWRTASLPQHGIEDIIMTDGTYGVRYSSAQIDGREKWS 63

Query: 70  QDFAGFLNVVNQRAKDVEIAWRPMK-----------PATCFPNGSSFACSWDVALANQLG 118
            D   F++V+ Q A    +A    K           PATCFPNGSS ACSWDV L +Q+G
Sbjct: 64  MD--DFISVITQTADQASVAEPAAKGGSEALFSTSLPATCFPNGSSLACSWDVELVHQMG 121

Query: 119 DALGKECQQMGVHLLLGPGINIRRTPLGGRSYEYYSEDPLISGEIASGVIHGLQQQGVGA 178
            ALG+ECQQMGV +LLGPGINIRRTPL GR YEYY+EDP++SG+IA+ +I+GLQQ+GVGA
Sbjct: 122 QALGRECQQMGVGILLGPGINIRRTPLAGRGYEYYAEDPVVSGDIAAALINGLQQEGVGA 181

Query: 179 SLKHFACNNSEIERTSMDSIVDERALREIYLRGFERAIKQARPWTVMSSYNRLNGAQTAE 238
           SLKHFA NNSE  RT MDSI++ERALREIYL GF+RAI ++RPWTVMSSYNRLNG QT++
Sbjct: 182 SLKHFAANNSEFRRTEMDSIIEERALREIYLAGFQRAIAKSRPWTVMSSYNRLNGVQTSQ 241

Query: 239 HSWLLTDVLRHEWGFDGVVVADWHGIKDRPQSLLAGNDLDMPESQSRKADLVKAINAGSV 298
             +LLT VLR EWG+DG+V++DW+GIKDRP SL+AGNDL MPE++  K  L+ AI A  V
Sbjct: 242 DPFLLTQVLRDEWGYDGLVMSDWYGIKDRPASLMAGNDLAMPETRRDKQTLLAAIEAEEV 301

Query: 299 PREQAELSATRVMRLVHRALHSEKRDTQCDKPTHHLLARRMVAESIVLLKNRNRALPLES 358
           P    + +  R++ L+ +     +  T+ D   HH LA+R+  ESIVLLKN    LPL S
Sbjct: 302 PMAVVDRACLRMLELLDKVQRHRRPQTRADFTAHHALAQRLAGESIVLLKNEEALLPLRS 361

Query: 359 ATCPRLLIVGEGAKKPVIQGSGCATTLPTQVDIPFDEMLKYAGDAIRVEWCRGHSD---D 415
              PR+ ++G+ A++PVIQGSGCATT+P  +D P DE+   AGD   V W  G  D   D
Sbjct: 362 EKTPRIAVLGKPAQEPVIQGSGCATTVPYLLDRPLDEIFDLAGDDFSVTWAVGAPDDLRD 421

Query: 416 PNQALALRDEACAAAREADRVVVFANSEDGYDGEGSDRLTLGLQAGQDALISALAAVNDN 475
             QALA   +AC+ A+EAD  V+F ++  G DGE  DR  L +    + LI  +AAV  N
Sbjct: 422 DEQALA---QACSVAQEADVAVLFVSTAVGEDGENGDRQDLHILPVHERLIREVAAVQPN 478

Query: 476 VIVVLANPDAVVMPWLEQVAAVVETFYAGQAMGGGLADVLFGVVNPSGKLTVTFPQQIAD 535
           ++VVLAN DAVVMPWL +  A++ETF+AGQ MG  +A++LFG  NP GKLTVT P  + +
Sbjct: 479 IVVVLANSDAVVMPWLGECKALLETFFAGQGMGRAVAEILFGKRNPCGKLTVTVPNSLEE 538

Query: 536 IPGWHSYPGENGRHYYSEGVFVGYRWYDVRHLEPLFPFGFGLSYSDFRYSDIAVDKAQVK 595
            P W  YPGEN RHYY EG+FVGYR+YD R L P FPFGFGLSY+ F Y +IA+  +++ 
Sbjct: 539 TPAWLHYPGENLRHYYGEGLFVGYRYYDKRRLMPQFPFGFGLSYTRFAYDNIALSASRLG 598

Query: 596 AGEEIHVSFTLTNASQRAGKEVCQLYSAYVDSRQKRPLRELRAFTKVLLQPGEQRRITLC 655
           A E + VSF LTN  + AGKE+ QLY +       R ++ L+AF+KV L  GE RR++L 
Sbjct: 599 ADETLTVSFDLTNCGEYAGKEIVQLYVSAPKGELIREVQSLKAFSKVALAAGESRRVSLQ 658

Query: 656 VPADDLRYYDTARQQWVLEAGQVQLCVGASSRDLPLAVTLTCLNKVARYRLIARDTQPKF 715
           +P  +L  Y      W++  G  Q+ VGASSRDLPL   +  ++   RY  +  D   + 
Sbjct: 659 LPIAELACYHPGLGDWMVTPGIWQIRVGASSRDLPLTAEME-VDCPQRYVPLRDDNSLQQ 717

Query: 716 ILENPLARGLFNAFLQQQLAVSAEDA-DRLLEHCANSFVGIMTTFDRRFRYRFDEQAMDA 774
           +++ P A       +  +  + AE   ++L+    + F G++           +   ++A
Sbjct: 718 LIQQPEAFARVVTLIADKSQIPAEQVREKLIRLAPDLFCGLLIALTEFLALDIERDELNA 777

Query: 775 VI 776
           V+
Sbjct: 778 VL 779


Lambda     K      H
   0.320    0.135    0.407 

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: 1500
Number of extensions: 52
Number of successful extensions: 2
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: 790
Length of database: 785
Length adjustment: 41
Effective length of query: 749
Effective length of database: 744
Effective search space:   557256
Effective search space used:   557256
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources