GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ams in Shewanella loihica PV-4

Align Alpha-glucosidase; EC 3.2.1.20 (characterized, see rationale)
to candidate 5209418 Shew_1889 alpha amylase, catalytic region (RefSeq)

Query= uniprot:H3K096
         (538 letters)



>FitnessBrowser__PV4:5209418
          Length = 541

 Score =  656 bits (1692), Expect = 0.0
 Identities = 296/502 (58%), Positives = 374/502 (74%), Gaps = 1/502 (0%)

Query: 3   DNMMWWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLD 62
           + + WWRG VIYQIYPRS +DS GDGVGDL GI  KLDY+ASLNVD IW+SPFF SPM D
Sbjct: 2   NQLSWWRGAVIYQIYPRSLMDSNGDGVGDLQGIISKLDYIASLNVDAIWISPFFKSPMKD 61

Query: 63  FGYDVSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTN 122
           FGYD+SDYR +DP+FGT+ DF  L++KAH LG+KV+IDQV+SHTSDQH WF ESRQ+R N
Sbjct: 62  FGYDISDYRAIDPLFGTMADFDELIDKAHGLGIKVIIDQVLSHTSDQHAWFSESRQSRDN 121

Query: 123 PKADWFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQ 182
            K DW+VWADP PDGT PNNWL+IFGG AW ++ RRQQYYLHNFLTSQPD+NFH+P+ RQ
Sbjct: 122 AKQDWYVWADPNPDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLTSQPDLNFHNPDVRQ 181

Query: 183 AQLDNMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVY 242
           A LDN++FWLD GVDGFRLD + F +HD +LRDNPP P+ + +  G  E NPY +Q H Y
Sbjct: 182 AVLDNVKFWLDKGVDGFRLDAITFCYHDEQLRDNPPKPEDKRQGRGFSEDNPYAYQYHYY 241

Query: 243 DLSRPENLDFLKDLRALMDEYPGTTTVGEIGDDNPLERMAEYTAGGDKLHMAYTFDLLNM 302
           + +RP+ + F+++LRAL+++YPG  T+GE+  ++ L  MAEYT G D+LHMAY+F+LL  
Sbjct: 242 NNTRPQTVGFIEELRALINQYPGVVTLGEVSSEDSLATMAEYTQGDDRLHMAYSFELLTD 301

Query: 303 PHSASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRWGADEDPHAYPKVMLAVLFSLR 362
             S +Y+R  +E  ++  GD WPCWA  NHDV R ATRWG D       K++ A+L SLR
Sbjct: 302 DFSPAYIRHTVEALEQSIGDGWPCWAIGNHDVQRVATRWGRDAFNSDMAKMLNAMLCSLR 361

Query: 363 GSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWT-DGEQGGFSPVE 421
           GSVC YQGEELGL E ++ +E++QDP+G   WP FKGRDGCRTPMPW  D    GFS   
Sbjct: 362 GSVCSYQGEELGLGEVEIAYEQLQDPFGITFWPMFKGRDGCRTPMPWRHDANHAGFSDNT 421

Query: 422 PWLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTR 481
           PWLP+ A H  +AV  Q+ +P + LN  R +LA+R+ HP L  GD+  ++  D LL F R
Sbjct: 422 PWLPVPADHKAVAVDVQEANPESILNHYRHMLAWRKLHPILVTGDIKFIESTDALLVFER 481

Query: 482 QKGDETLLCVFNLTGQEQQTTL 503
           + G++TLL  FNL+GQ Q  +L
Sbjct: 482 RLGEQTLLVAFNLSGQPQSFSL 503


Lambda     K      H
   0.320    0.138    0.443 

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: 1031
Number of extensions: 43
Number of successful extensions: 2
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: 538
Length of database: 541
Length adjustment: 35
Effective length of query: 503
Effective length of database: 506
Effective search space:   254518
Effective search space used:   254518
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: 52 (24.6 bits)

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

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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:

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:

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:

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:

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