Alignments for a candidate for treF in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Halomonas desiderata SP1

Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate WP_086508167.1 BZY95_RS01125 DUF3459 domain-containing protein

Query= uniprot:A8LLL3
         (552 letters)



>NCBI__GCF_002151265.1:WP_086508167.1
          Length = 558

 Score =  601 bits (1550), Expect = e-176
 Identities = 305/538 (56%), Positives = 358/538 (66%), Gaps = 11/538 (2%)

Query: 18  DWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVDAIWISPFFTSPMKDFGY 77
           DWWRGAVIYQIYPRSF DSNGDGIGDL GI++++ YIASL VDAIWISPFFTSPMKDFGY
Sbjct: 13  DWWRGAVIYQIYPRSFMDSNGDGIGDLPGIIDKLDYIASLNVDAIWISPFFTSPMKDFGY 72

Query: 78  DISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSDQHPWFEESRSSRDNPKA 137
           D++DY  VDP+FG+L DFD L+E AH  GL+V ID VLSHTSD+HPWF ESR SRDNPKA
Sbjct: 73  DVADYRSVDPIFGTLDDFDRLVEAAHARGLKVTIDQVLSHTSDRHPWFSESRGSRDNPKA 132

Query: 138 DWYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLTSQPDLNFHCADVQDALL 197
           DWYVWA+AK DG+PP NW S+FGGS W WD RRCQYYLHNFL SQPDLNF    V +A+L
Sbjct: 133 DWYVWAEAKADGSPPTNWQSVFGGSAWQWDTRRCQYYLHNFLDSQPDLNFRNPAVVEAVL 192

Query: 198 GVGRFWLDRGVDGFRLDTINFYVHDAELRDNPP-LPPEERNSNIAPEVNPYNHQRHLYSK 256
              RFWLDRGVDGFRLD +NF  H  EL DNPP     E    + P+ NPY +Q HL+ K
Sbjct: 193 DEVRFWLDRGVDGFRLDAVNFCTH-GELVDNPPRSDAAEGFLGVRPD-NPYGYQLHLHDK 250

Query: 257 NQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRGETGVHMCYAFEFLAQE 316
            QPENL FL K RA+++EYP   +VGEVGD    L ++  YT+G   +HM Y+F+ L  E
Sbjct: 251 TQPENLAFLEKLRALLDEYPGTTSVGEVGDDD-SLNVMAAYTQGNKRLHMAYSFDLLG-E 308

Query: 317 KLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRWDL--TPGAQRGMLTLLMCLRG 374
           +     +   +  ++    DGW CWA  NHDV R  +RW     P   R  L  L+  RG
Sbjct: 309 RHDPDFLHRTMTAMEAKIGDGWPCWALGNHDVPRLATRWKAQDDPDRLRLYLAFLLTQRG 368

Query: 375 SVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVWQSDNMSGGFSIHRP 434
           SVCLYQGEELGLPEAE+  + L DP GI FWP YKGRDGCRTP  W  D   G FS   P
Sbjct: 369 SVCLYQGEELGLPEAELTLEQLVDPAGITFWPAYKGRDGCRTPHPWCGDTRHGDFSQGEP 428

Query: 435 WLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDISDVTVVGDVISFLR- 493
           WLPV   HL LA+  Q+EAPD+LL+ YR  LAFRR H AL KG++    V  +V+   R 
Sbjct: 429 WLPVPEAHLELAMRHQDEAPDSLLNAYRAFLAFRREHVALKKGEVRYHPVRDEVLCLERH 488

Query: 494 ---KDPEETVFVAINMSDAPGAVDLPPGNWMQIGAELNSGGTSPDGRVHLGPWQPCIA 548
              + P E + VA+N SDAP  +  P        A     G   +G V L P    IA
Sbjct: 489 HPARAPNERLLVALNFSDAPRTLPAPRQARPLDDAPALVNGVWANGEVQLPPCGIAIA 546


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: 1151
Number of extensions: 54
Number of successful extensions: 6
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: 558
Length adjustment: 36
Effective length of query: 516
Effective length of database: 522
Effective search space:   269352
Effective search space used:   269352
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 24 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