Alignments for a candidate for lacZ in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Stenotrophomonas chelatiphaga DSM 21508

Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate WP_057508205.1 ABB28_RS08430 beta-glucosidase

Query= SwissProt::E7CY69
         (757 letters)



>NCBI__GCF_001431535.1:WP_057508205.1
          Length = 724

 Score =  226 bits (575), Expect = 4e-63
 Identities = 200/643 (31%), Positives = 290/643 (45%), Gaps = 76/643 (11%)

Query: 36  GIPSYMITDGPHGLRKSLASSAGETDLDDSVPATCFPPAAGLSSSWNPELIHKVGEAMAE 95
           GIP  +  D  HG+R                  T FP   G ++S+ PEL  +   A A 
Sbjct: 83  GIPVILAADVIHGMR------------------TVFPIPLGEAASFEPELARRTARATAV 124

Query: 96  ECIQEKVAVILGPGVNIKRNPLGGRCFEYWSEDPYLAGHEAIGIVEGVQSKGVGT----- 150
           E     +     P V+I R+   GR  E   ED  L    A   V G Q   +       
Sbjct: 125 EATAAGLHWTYAPAVDIARDQRWGRGAEGAGEDVVLGCAFAAARVRGFQGDDLRAHDALL 184

Query: 151 -SLKHFAANNQETDRLRVD-ARISPRALREIYFPAFEHIVKKAQPWTIMCSYNRINGVHS 208
            + KHFAA       +  +   ISP+ LR+++ P F+     A   T+M S+N INGV +
Sbjct: 185 ATPKHFAAYGAVMAGMEYNMVDISPQTLRDVHLPPFKAAFD-AGAITVMSSFNDINGVPA 243

Query: 209 AQNHWLLTDVLRDEWGFDGIVMSDWGAD----------HDRGAS---LNAGLNLEMPPSY 255
           + N  LLTD+LR EW F G+V+SD+ AD           DR A+     AGL+L M   +
Sbjct: 244 SANAELLTDILRGEWNFPGVVISDYTADMELVAHGYAADDRDATAKAFTAGLDLSMQSGF 303

Query: 256 TDDQIVYAVRDGLITPAQLDRMAQGMIDLVNKTRAAMSIDNYRF----------DVDAHD 305
             + +   V  G +  A LD   + ++ L  K    +  D YR            + AH+
Sbjct: 304 YAEHLPGLVESGEVPMAVLDEGVRRILWL--KETIGLFDDPYRSLDPAREADNSHIAAHE 361

Query: 306 EVAHQAAIESIVMLKNDDAILPLNAGPVANPSATPQKIAVIGEFARTPRYQGGGSSHITP 365
            ++  AA  SIV+LKN+ + LPL            QKIA+IG F +  R    G   +  
Sbjct: 362 ALSRDAARRSIVLLKNEQSALPLRRDG--------QKIALIGPFVQD-RENIEGCWTLFG 412

Query: 366 TKMTSFLDTLAERGIKADFAPGFTLDLEPADPALES-------EAVETAKNADVVLMFLG 418
            K + ++D   E G++A       L++ P    LES        AV  A  ADVV++ LG
Sbjct: 413 DK-SRYVDL--ETGVRAAIGDEALLEVVPGCE-LESGIAGGIEAAVAAALRADVVVLALG 468

Query: 419 LPEAVESEGFDRDTLDMPAKQIALLEQVAAANQNVVVVLSNGSVITVAPWAKNAKGILES 478
            P+    E   R  + +P  Q AL E VA A + +VV+L NG  + +    +NA+ +  +
Sbjct: 469 EPQRYSGEAQSRVEITLPPAQQALAEAVAMAGKPMVVLLRNGRALALQGAVRNAQAVAIT 528

Query: 479 WLLGQSGGPALADVIFGQVSPSGKLAQSIPLDINDDPSMLNWPGEEGHVDYGEGVFAGYR 538
           W LG   G A+ADV+FG  +PS +L  S P      P   N P   G  +         R
Sbjct: 529 WYLGTQTGHAVADVLFGDYNPSARLPVSFPQVSGQQPYFYNHP-RTGRPELPTMSEFKAR 587

Query: 539 YYDTYGKAVDYPFGYGLSYATFEITGVAVAKTGA---NTATVTATVTNTSDVDAAETVQV 595
           + +   + + Y FG+G+SY +F      ++ T     +T T+T T+TNT  V   E VQ+
Sbjct: 588 WREIPNEPL-YAFGHGISYTSFAYGVPQLSSTRLGWDDTLTITTTLTNTGSVAGEEVVQL 646

Query: 596 YVVPGKADVARPKHELKGFTKAFLKAGESKTVAIDLDERAFAY 638
           Y+    A   RP  ELK F K  L+ GES  V+  +     A+
Sbjct: 647 YIHDRVASRVRPVRELKDFRKVMLQPGESTEVSFSVQRSQLAF 689


Lambda     K      H
   0.315    0.132    0.393 

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: 1195
Number of extensions: 60
Number of successful extensions: 8
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: 757
Length of database: 724
Length adjustment: 40
Effective length of query: 717
Effective length of database: 684
Effective search space:   490428
Effective search space used:   490428
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: 42 (22.0 bits)
S2: 55 (25.8 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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