Alignments for a candidate for susB in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Cereibacter sphaeroides ATCC 17029

Align α-glucosidase (AglA;HaG) (EC 3.2.1.20) (characterized)
to candidate WP_011840128.1 RSPH17029_RS00200 DUF3459 domain-containing protein

Query= CAZy::BAL49684.1
         (538 letters)



>NCBI__GCF_000015985.1:WP_011840128.1
          Length = 536

 Score =  591 bits (1524), Expect = e-173
 Identities = 297/533 (55%), Positives = 359/533 (67%), Gaps = 13/533 (2%)

Query: 7   WWRGGVIYQIYPRSFLDSRGDGVGDLNGITEKLDYVASLNVDGIWLSPFFTSPMLDFGYD 66
           WWRG V YQIYPRSF DS GDGVGDL GI E+LD+VA L  D IWLSP F SPM D GYD
Sbjct: 4   WWRGSVTYQIYPRSFQDSDGDGVGDLRGIIERLDHVAWLGADAIWLSPIFPSPMEDMGYD 63

Query: 67  VSDYRDVDPMFGTLEDFKALLEKAHSLGLKVMIDQVISHTSDQHPWFQESRQNRTNPKAD 126
           VSDY  + P+FG++EDF ALL +AH LGLKV+IDQV+SH+S  HP+F+ESR++R NPKAD
Sbjct: 64  VSDYTAIHPLFGSMEDFDALLARAHELGLKVIIDQVLSHSSSAHPFFRESRRSRDNPKAD 123

Query: 127 WFVWADPKPDGTPPNNWLSIFGGSAWTFDSRRQQYYLHNFLTSQPDVNFHHPEARQAQLD 186
           W+VWAD +PDG+PPNNWLS+FGGSAW +D++R+QYYLHNFL SQPD NFH+PE +   LD
Sbjct: 124 WYVWADAQPDGSPPNNWLSVFGGSAWEWDAQRRQYYLHNFLISQPDFNFHNPEVQDWLLD 183

Query: 187 NMRFWLDLGVDGFRLDTVNFYFHDAELRDNPPVPKGEAKTLGAPEANPYTWQRHVYDLSR 246
            MRFWLD GVDGFRLDTVNFYFHDAELR N P P+        P  N Y  Q H +  SR
Sbjct: 184 QMRFWLDRGVDGFRLDTVNFYFHDAELRSNRPNPQNGP----IPPVNAYDMQDHAFSKSR 239

Query: 247 PENLDFLKDLRALMDEYPGTTTVGEIGDD-NPLERMAEYTAGGDKLHMAYTFDLLNMPHS 305
            EN+ FL  +R L+D+YP    VGE+ D    L  MAEYT+G D+LHMAYTF++L+   +
Sbjct: 240 IENIAFLLRMRKLLDDYPDRAMVGEVADGLRGLAIMAEYTSGADRLHMAYTFEMLSRTFT 299

Query: 306 ASYLREVIERFQRLAGDAWPCWATSNHDVVRSATRW---GADEDPHAYPKVMLAVLFSLR 362
           A + R  IE F   A   WPCWA SNHDVVR ATRW   GA++D     ++  A+L S  
Sbjct: 300 AGHFRSRIEEFFATAPHGWPCWAFSNHDVVRHATRWAGHGAEDD---VARLAAAMLLSFE 356

Query: 363 GSVCLYQGEELGLPEADVPFERIQDPYGKVLWPEFKGRDGCRTPMPWTDGEQGGFSPVEP 422
           GSV LYQGEELG  E ++ +E + DP G   WPE KGRDGCRTPM W DG  GGF+   P
Sbjct: 357 GSVSLYQGEELGQTETELLYEELTDPPGLRFWPEEKGRDGCRTPMVWDDGPAGGFTTGTP 416

Query: 423 WLPMEARHLELAVSRQQDDPNATLNTVRALLAFRRSHPALFDGDLSLVDVGDDLLGFTRQ 482
           WLP++   L   V+ Q+  P + L T RALL FRR+ PAL  G     D+ + +LGFTR 
Sbjct: 417 WLPVKPPQLARNVASQKGIPGSVLETYRALLQFRRTQPALIRGRSRFFDLPEPMLGFTRT 476

Query: 483 KGDETLLCVFNLTGQEQQTTLPVEVASDLPVAHFTATRDGSTLTLPAYQAAFM 535
              ++L C FNL  +    TLP       P     A  +G  LTL A   AF+
Sbjct: 477 LDGQSLACFFNLGIEPVSATLPGHGGLIGPAQ--AAVLEGDRLTLGANGYAFL 527


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: 1027
Number of extensions: 52
Number of successful extensions: 3
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: 536
Length adjustment: 35
Effective length of query: 503
Effective length of database: 501
Effective search space:   252003
Effective search space used:   252003
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 Apr 10 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 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