Alignments for a candidate for susB in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Sinorhizobium meliloti 1021

Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate SMc01532 SMc01532 alpha-glycosylase

Query= uniprot:A8LLL3
         (552 letters)



>FitnessBrowser__Smeli:SMc01532
          Length = 547

 Score =  648 bits (1672), Expect = 0.0
 Identities = 305/507 (60%), Positives = 367/507 (72%), Gaps = 6/507 (1%)

Query: 15  ADPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKD 74
           +D +WWRGAVIYQ+YPRSFQD++GDG+GDL G+  R+P+IASLGVDAIW+SPFFTSP  D
Sbjct: 7   SDENWWRGAVIYQVYPRSFQDTDGDGMGDLRGVTRRLPHIASLGVDAIWLSPFFTSPQAD 66

Query: 75  FGYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDN 134
            GYD+SDY DVDPMFG+LADFD ++  AH  GL+V+ID V+SHTSD+HPWF ESRSSR N
Sbjct: 67  MGYDVSDYCDVDPMFGTLADFDEMLAEAHRLGLKVIIDQVISHTSDRHPWFVESRSSRTN 126

Query: 135 PKADWYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQD 194
            KADWYVWAD KPDGT PNNWLSIFGG GW WD  R QYYLHNFL+SQPDLNFH  +VQ+
Sbjct: 127 AKADWYVWADPKPDGTAPNNWLSIFGGPGWEWDGVRRQYYLHNFLSSQPDLNFHNPEVQE 186

Query: 195 ALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPE-ERNSNIAPEVNPYNHQRHL 253
           A+L   RFWLDRGVDGFRLDT NFY HD  LRDNPPL P+ +  S  APEVNPY  Q HL
Sbjct: 187 AVLATVRFWLDRGVDGFRLDTANFYFHDRLLRDNPPLVPDPDATSRDAPEVNPYGMQDHL 246

Query: 254 YSKNQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFL 313
           Y K QPENL+FL +FRA+++EY   A VGEVGD    L+ +  YT G   +HMCY F+ L
Sbjct: 247 YDKTQPENLDFLRRFRAVLDEYGGRATVGEVGDGSRSLQTVAAYTSGGDKLHMCYTFDLL 306

Query: 314 AQEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRWDLTPGAQRGM----LTLL 369
             E  TA+     +       +DGW CWAFSNHDVMRHVSR+ L    +  +    ++LL
Sbjct: 307 GPE-FTARHFRRCVENFQSTVTDGWVCWAFSNHDVMRHVSRFALREADRERVAKLAISLL 365

Query: 370 MCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGF 429
             LRG++CLYQGEELGLPEAE+AF++L+DPYGI FWP + GRDGCRTPMVW+ +  + GF
Sbjct: 366 ASLRGTICLYQGEELGLPEAELAFEELRDPYGIRFWPAFAGRDGCRTPMVWERELSNAGF 425

Query: 430 SIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDVI 489
           S   PWLPV   H  LAV  QE    A+L HYR+ L FRRA  ALV GD+  +    D++
Sbjct: 426 SAGTPWLPVRDGHRMLAVDAQEGVEGAVLEHYRQTLGFRRAQSALVDGDMVFLGTNQDLL 485

Query: 490 SFLRKDPEETVFVAINMSDAPGAVDLP 516
            F R+  +E +    N++  P    LP
Sbjct: 486 VFTREKDDERLLFVFNLTQEPQTFHLP 512


Lambda     K      H
   0.321    0.138    0.451 

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: 1046
Number of extensions: 37
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: 552
Length of database: 547
Length adjustment: 36
Effective length of query: 516
Effective length of database: 511
Effective search space:   263676
Effective search space used:   263676
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: 53 (25.0 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