Alignments for a candidate for lacZ in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Sinorhizobium meliloti 1021

Align β-galactosidase (EC 3.2.1.23) (characterized)
to candidate SM_b20966 SM_b20966 beta-galactosidase

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



>FitnessBrowser__Smeli:SM_b20966
          Length = 646

 Score =  656 bits (1692), Expect = 0.0
 Identities = 334/646 (51%), Positives = 410/646 (63%), Gaps = 5/646 (0%)

Query: 4   VCYYPEHWPKERWKEDARRMREAGLSHVRIGEFAWALLEPEPGRLEWGWLDEAIATLAAE 63
           +CYYPE WP+ +W EDARRM E GLS VRIGEFAWA +EP  G   W WLDEAI  L   
Sbjct: 1   MCYYPEQWPRGKWAEDARRMVELGLSWVRIGEFAWAKIEPRSGEFHWEWLDEAIDVLGKA 60

Query: 64  GLKVVLGTPTATPPKWLVDRYPEILPVDREGRRRRFGGRRHYCFSSPVYREEARRIVTLL 123
           GLKV+LGTPTA PPKWLV+RYPEILPVD  G  R+FG RRHYCFSS  YR EA RI   +
Sbjct: 61  GLKVILGTPTAAPPKWLVNRYPEILPVDATGAVRKFGARRHYCFSSRRYRSEAARITEAM 120

Query: 124 AERYGGLEAVTGFQTDNEYGCHDTVRCYCPRCQEAFRGWLEARYGTIEALNEAWGTAFWS 183
           A RYG    V  +QTDNEYG HDT+  Y      AFR WL  RYG+I+ LN AWGT+FWS
Sbjct: 121 ARRYGEHIYVHAWQTDNEYGDHDTIYSYSAEAVGAFRLWLAERYGSIDELNRAWGTSFWS 180

Query: 184 QRYRSFAEVELPHLTVAEPNPSHLLDYYRFASDQVRAFNRLQVEILRAHAPGKFVTHNFM 243
            RY SF E++LP+  V EP+P+H +D+ RF+SDQV++FN+ QV+I+RAH+PG+ VTHNFM
Sbjct: 181 MRYDSFEEIDLPNNLVEEPSPTHGVDFIRFSSDQVKSFNKAQVDIIRAHSPGRPVTHNFM 240

Query: 244 GFFTDLDAFALAQDLDFASWDSYPLGFTDLMPLPPEEKLRYARTGHPDVAAFHHDLYRGV 303
              TD D + + +D+D ASWD YP+G      L  ++K  Y R G PD  AF+HDLYR V
Sbjct: 241 SQNTDFDHYRVGEDIDIASWDVYPMGGLLNGRLAAKDKEHYLRVGDPDQPAFNHDLYRAV 300

Query: 304 GRGRFWVMEQQPGPVNWAPHNPSPAPGMVRLWTWEALAHGAEVVSYFRWRQAPFAQEQMH 363
           GRGR WVMEQQPGPVNWA HN SPA GMVRLWTW A AHG ++VSYFRWRQAPFAQEQ H
Sbjct: 301 GRGRVWVMEQQPGPVNWAAHNQSPADGMVRLWTWLAYAHGVDMVSYFRWRQAPFAQEQFH 360

Query: 364 AGLHRPDSAPDQGFFEAKRVAEELAALALPPV-AQAPVALVFDYEAAWIYEVQPQGAEWS 422
           AGL  P+S  DQG+ E   V  E+  L    V  +A VA+V DYE+ W   V PQG  +S
Sbjct: 361 AGLLLPNSEADQGYLEVAEVVAEMKRLPEGEVRGKAQVAIVLDYESRWATRVLPQGRSYS 420

Query: 423 YLGLVYLFYSALRRLGLDVDVVPPGASLRGYAFAVVPSLPIVREEALEAFREAEGPVLFG 482
              +   +YS + RLG+DVD +   + + GY   + P L I  E  +E    A+  V+FG
Sbjct: 421 ASAVALDWYSTVARLGVDVDFIGQHSDIAGYKLILAPDLVIAEEAFVERLTRADAKVVFG 480

Query: 483 PRSGSKTETFQIPKELPPGPLQALLPLKVVRVESLPPGLLEVAEGALGRFPLGLWREWVE 542
            RSGSKT    IP+ LPPGPL  L+ + V RVESLP    E        +  G WRE V 
Sbjct: 481 ARSGSKTRDMHIPEGLPPGPLAKLIDISVSRVESLPEFHSETVLYGNEAYEAGGWRETVR 540

Query: 543 APLKPLLTF----QDGKGALYREGRYLYLAAWPSPELAGRLLSALAAEAGLKVLSLPEGL 598
                + +F    ++G  AL    +  YLA   +  L  +++      AGL+ L     L
Sbjct: 541 TSETVIASFDGEYRNGAPALVGSDKARYLAVAANGALLDKVIGDALGWAGLESLPDLGDL 600

Query: 599 RLRRRGTWVFAFNYGPEAVEAPASEGARFLLGSRRVGPYDLAVWEE 644
           R+ RRG   FAFN+G    E PA   A F +G R + P D+A+W E
Sbjct: 601 RVTRRGNLRFAFNFGRIPAEVPAGASAEFYVGGRTLKPVDVAIWRE 646


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: 1400
Number of extensions: 69
Number of successful extensions: 5
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: 646
Length adjustment: 38
Effective length of query: 607
Effective length of database: 608
Effective search space:   369056
Effective search space used:   369056
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 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)
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 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