Alignments for a candidate for susB in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Pedobacter sp. GW460-11-11-14-LB5

Align α-glucosidase / glucoamylase (SusB;BtGH97a;BT3703;BT_3703) (EC 3.2.1.3) (characterized)
to candidate CA265_RS15710 CA265_RS15710 alpha-glucosidase

Query= CAZy::AAC44671.1
         (738 letters)



>FitnessBrowser__Pedo557:CA265_RS15710
          Length = 701

 Score = 1023 bits (2644), Expect = 0.0
 Identities = 496/721 (68%), Positives = 578/721 (80%), Gaps = 29/721 (4%)

Query: 9   LIAFLC-ISFIANA-----QQKLTSPDNNLVMTFQVDSKGAPTYELTYKNKVVIKPSTLG 62
           ++  +C + F  NA      + L SPD NLV++F +   G PTY L YK K VIK S LG
Sbjct: 1   MLTLICTVLFFGNAFGNVPGEDLKSPDGNLVVSFALAEGGVPTYSLKYKGKDVIKTSKLG 60

Query: 63  LELKKEDNTRTDFDWVDRRDLTKLDSKTNLYDGFEVKDTQTATFDETWQPVWGEEKEIRN 122
           LELK                    D K+ L DGF + DT+T+ F+ETW+PVWGE KEI N
Sbjct: 61  LELK--------------------DGKS-LLDGFTITDTKTSAFNETWKPVWGEVKEIVN 99

Query: 123 HYNELAVTLYQPMNDRSIVIRFRLFNDGLGFRYEFPQQKSLNYFVIKEEHSQFGMNGDHI 182
           HYNELAVTL Q   +R I++R RLFNDGLGFRYEFP+QK+L YFVIKEE +QF + GDH 
Sbjct: 100 HYNELAVTLTQKETNRYIIVRLRLFNDGLGFRYEFPEQKNLAYFVIKEEKTQFALAGDHK 159

Query: 183 AFWIPGDYDTQEYDYTISRLSEIRGLMKEAITPNSSQTPFSQTGVQTALMMKTDDGLYIN 242
           AFW+PGDYDTQEY    S LSE+RG MK A+TPN+SQT FS TG+QT LMMK+ DGLYIN
Sbjct: 160 AFWLPGDYDTQEYSTVTSNLSEVRGKMKAAVTPNASQTTFSPTGLQTPLMMKSKDGLYIN 219

Query: 243 LHEAALVDYSCMHLNLDDKNMVFESWLTPDAKGDKGYMQTPCNTPWRTIIVSDDARNILA 302
           +HEAAL++YS M LNLDDKNMV ESWLTPDA GDKGYMQ PC +PWRTIIVSD A +IL 
Sbjct: 220 IHEAALINYSLMSLNLDDKNMVLESWLTPDAIGDKGYMQAPCLSPWRTIIVSDKAGDILT 279

Query: 303 SRITLNLNEPCKIADAASWVKPVKYIGVWWDMITGKGSWAYTDELTSVKLGETDYSKTKP 362
           S++T NLNE  K  D  SW+KP KY+GVWW+MITGK +WAY D LTSV+LG TDY+KTKP
Sbjct: 280 SKLTYNLNEATKFKDV-SWIKPTKYVGVWWEMITGKSTWAYND-LTSVQLGVTDYAKTKP 337

Query: 363 NGKHSANTANVKRYIDFAAAHGFDAVLVEGWNEGWEDWFGNSKDYVFDFVTPYPDFDVKE 422
           NGKH+ANTA+VK YIDFAA +G DAVLVEGWNEGWEDWFG +KD VFDFVTPYPDFDVKE
Sbjct: 338 NGKHAANTAHVKEYIDFAAKNGLDAVLVEGWNEGWEDWFGKTKDDVFDFVTPYPDFDVKE 397

Query: 423 IHRYAARKGIKMMMHHETSASVRNYERHMDKAYQFMADNGYNSVKSGYVGNIIPRGEHHY 482
           +HRYAA KGIKM+MHHETS+SVRNYERH+D AY+FM  NGY++VKSGYVGN+IPRGEHHY
Sbjct: 398 LHRYAASKGIKMIMHHETSSSVRNYERHLDTAYKFMKANGYDAVKSGYVGNMIPRGEHHY 457

Query: 483 GQWMNNHYLYAVKKAADYKIMVNAHEATRPTGICRTYPNLIGNESARGTEYESFGGNKVY 542
           GQW+NNHYLYA++KAA+YKIMVNAHEA RPTG+ RTYPNLIGNESARGTEYE+FGGN   
Sbjct: 458 GQWLNNHYLYAIQKAAEYKIMVNAHEAVRPTGLARTYPNLIGNESARGTEYEAFGGNNAD 517

Query: 543 HTTILPFTRLVGGPMDYTPGIFETHCNKMNPANNSQVRSTIARQLALYVTMYSPLQMAAD 602
           HTTILPFTRL+GGPMDYTPGIFET  +  NP N S V ST+ARQLALYVTMYSPLQMAAD
Sbjct: 518 HTTILPFTRLIGGPMDYTPGIFETKVSVYNPENISFVHSTLARQLALYVTMYSPLQMAAD 577

Query: 603 IPENYERFMDAFQFIKDVALDWDETNYLEAEPGEYITIARKAKDTDDWYVGCTAGENGHT 662
           +PE Y ++MDAFQFIKDVA+DWD+T  LEAEPG+YIT ARKAK  ++W+VG T  E   T
Sbjct: 578 LPETYNKYMDAFQFIKDVAVDWDDTKVLEAEPGDYITFARKAKGKNNWFVGRTNDEVART 637

Query: 663 SKLVFDFLTPGKQYIATVYADAKDADWKENPQAYTIKKGILTNKSKLNLHAANGGGYAIS 722
           SK+ F FL PGK+Y AT+YADAKDA ++ NP+AYTI+K  ++NK+KL+ + A GGGYAIS
Sbjct: 638 SKIDFSFLDPGKKYTATIYADAKDAHYETNPKAYTIRKMEVSNKTKLSQYCAPGGGYAIS 697

Query: 723 I 723
           I
Sbjct: 698 I 698


Lambda     K      H
   0.317    0.134    0.411 

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: 1862
Number of extensions: 96
Number of successful extensions: 4
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: 738
Length of database: 701
Length adjustment: 40
Effective length of query: 698
Effective length of database: 661
Effective search space:   461378
Effective search space used:   461378
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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)
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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