Alignments for a candidate for lacZ in Methylocystis bryophila S285

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Methylocystis bryophila S285

Align β-galactosidase (EC 3.2.1.23) (characterized)
to candidate WP_085773771.1 B1812_RS16005 beta-galactosidase

Query= CAZy::ABI35985.1
         (645 letters)



>NCBI__GCF_002117405.1:WP_085773771.1
          Length = 654

 Score =  673 bits (1736), Expect = 0.0
 Identities = 354/650 (54%), Positives = 430/650 (66%), Gaps = 14/650 (2%)

Query: 2   LGVCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLA 61
           LGVCYYPEHWP++ W EDARRMR+ GLS VRIGEFAW+ LEPE GR ++ WL  AI  L 
Sbjct: 6   LGVCYYPEHWPEDLWTEDARRMRDVGLSVVRIGEFAWSRLEPEDGRYDFDWLARAIDVLH 65

Query: 62  AEGLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVT 121
             GL+VVLGTPTATPPKWLVD+ P++L  + +GR R FG RRHYCFS   Y  E  RIVT
Sbjct: 66  EAGLRVVLGTPTATPPKWLVDKMPDMLARNAQGRPRGFGSRRHYCFSYEPYARECERIVT 125

Query: 122 LLAERYGGLEAVTGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAF 181
            LA+ +G   AV  +Q DNEYGCHDTV  Y P  +EAFR W E +YG I ALN AWG  F
Sbjct: 126 ALAQAFGAHPAVVAWQIDNEYGCHDTVESYSPAAREAFRRWCEHKYGDIGALNRAWGNVF 185

Query: 182 WSQRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHN 241
           WS     F ++ELPHLTV E NP+ LLD+ RF+SDQV AF+R QVEI+R H+P + + HN
Sbjct: 186 WSMELSRFDQIELPHLTVTEANPACLLDFKRFSSDQVAAFHRRQVEIIRRHSPSRDILHN 245

Query: 242 FMGFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDLYR 301
           FMG FT  D FA+ +DLD A+WDSYPLGF +        K R+ R G PD  AFHHDLYR
Sbjct: 246 FMGAFTAFDHFAVGRDLDVAAWDSYPLGFLERSHRDEAFKRRFMRVGDPDFQAFHHDLYR 305

Query: 302 GVGRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQ 361
             G GR W+MEQQPG VNWAP NP PA G VRLW++EA A GAEVVSYFRWRQAPFAQEQ
Sbjct: 306 ACGAGRLWIMEQQPGAVNWAPWNPLPAKGAVRLWSFEAFAAGAEVVSYFRWRQAPFAQEQ 365

Query: 362 MHAGLHRPDSAPDQGFFEAKRVAEELAAL-ALPPVAQAPVALVFDYEAAWIYEVQPQGAE 420
           MH GL  P+S P++ +  A+ VA EL ++ A      A VALVFDY++A+ +E++PQG +
Sbjct: 366 MHEGLLLPNSEPNEAYHVARAVARELESIDAKVETECADVALVFDYDSAFAWEIEPQGQD 425

Query: 421 WSYLGLVYLFYSALRRLGLDVDVVPP-GASLRGYAFAVVPSLPIVREEALEAFREAEGPV 479
           +SY  L+  FY  LR+LGL+VDVVPP   ++      V P+L         AF E+   V
Sbjct: 426 FSYFDLILDFYGGLRKLGLNVDVVPPTPEAMARRKLIVAPALFASSAALTRAFSESGALV 485

Query: 480 LFGPRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGL---LEVAE-GALGRFPLG 535
           L GPRSGSKTE FQIP  LPPG  + L+ + + RVESL PG    +E AE GA  R    
Sbjct: 486 LLGPRSGSKTEDFQIPPGLPPGDFRPLVDVAIQRVESLRPGAQIPVEAAENGAFVR---- 541

Query: 536 LWREWVEAPLKP--LLTFQDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEAGLKVLS 593
            WRE + A  +   LL   DG  AL R  R+LYLA  P+  L   LL  LA EAGL ++ 
Sbjct: 542 -WREIIAAGAEAAVLLRCDDGAPALTRRERFLYLAGLPNDLLRDALLRRLANEAGLTLID 600

Query: 594 LPEGLRLRRRGTWVFAFNYGPEAVE-APASEGARFLLGSRRVGPYDLAVW 642
           LPE +RLR  G   + FNYG    + +P    A  LLG RR+ P  +A++
Sbjct: 601 LPEHIRLRDNGPMRYVFNYGERDFDLSPILGEASLLLGERRLPPCGVALF 650


Lambda     K      H
   0.322    0.139    0.454 

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: 1351
Number of extensions: 60
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: 645
Length of database: 654
Length adjustment: 38
Effective length of query: 607
Effective length of database: 616
Effective search space:   373912
Effective search space used:   373912
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 (21.9 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Apr 09 2024. 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)
SQLite3 databases

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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 2024 update 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