Alignments for a candidate for susB in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Flavobacterium beibuense F44-8

Align α-glucosidase / glucoamylase (SusB;BtGH97a;BT3703;BT_3703) (EC 3.2.1.3) (characterized)
to candidate WP_035135251.1 Q763_RS13600 glycoside hydrolase family 97 protein

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



>NCBI__GCF_000769915.1:WP_035135251.1
          Length = 714

 Score = 1066 bits (2756), Expect = 0.0
 Identities = 509/736 (69%), Positives = 602/736 (81%), Gaps = 24/736 (3%)

Query: 4   RKILSLIAFLCISFIANAQ-QKLTSPDNNLVMTFQVDSKGAPTYELTYKNKVVIKPSTLG 62
           +K++  + F C++ +ANA  Q+L SP+ N  + F + + G P Y LTYK K V+KPS LG
Sbjct: 2   KKVIFALCF-CLAVLANANAQELKSPNGNFNLKFFLQNDGTPAYSLTYKGKEVVKPSKLG 60

Query: 63  LELKKEDNTRTDFDWVDRRDLTKLDSKTNLYDGFEVKDTQTATFDETWQPVWGEEKEIRN 122
           LELK                    D + +L + F V DT+TA FDE W PVWGE K IRN
Sbjct: 61  LELK--------------------DDEKSLLNDFTVTDTKTAMFDENWTPVWGEVKTIRN 100

Query: 123 HYNELAVTLYQPMNDRSIVIRFRLFNDGLGFRYEFPQQKSLNYFVIKEEHSQFGMNGDHI 182
           HYNELAV+L Q   +R +VIRFRLF+DGLGFRYEFPQQK+L YF+IKEE +QF M GDH 
Sbjct: 101 HYNELAVSLNQKGTNRQMVIRFRLFDDGLGFRYEFPQQKNLVYFIIKEERTQFAMTGDHT 160

Query: 183 AFWIPGDYDTQEYDYTISRLSEIRGLMKEAITPNSSQTPFSQTGVQTALMMKTDDGLYIN 242
           A+WIPGDYDTQEYDYT+S+LSEIRGLM+++IT N SQ  FS TGVQT+LM+KTDDG+YIN
Sbjct: 161 AYWIPGDYDTQEYDYTVSKLSEIRGLMEKSITANVSQKSFSPTGVQTSLMLKTDDGIYIN 220

Query: 243 LHEAALVDYSCMHLNLDDKNMVFESWLTPDAKGDKGYMQTPCNTPWRTIIVSDDARNILA 302
           LHEAAL++Y+CMHLNLDDKNMVFESWLTPDA+G+KG++Q P NTPWRT+IVSDDAR+ILA
Sbjct: 221 LHEAALINYACMHLNLDDKNMVFESWLTPDAQGNKGHVQAPFNTPWRTVIVSDDARDILA 280

Query: 303 SRITLNLNEPCKIADAASWVKPVKYIGVWWDMITGKGSWAYTDELTSVKLGETDYSKTKP 362
           S+ITLNLNEPCK+ D  SW+KPVKYIGVWW+MITGK +WAYTD+L SV+LG TD+SK KP
Sbjct: 281 SKITLNLNEPCKLDDT-SWIKPVKYIGVWWEMITGKSTWAYTDDLPSVQLGITDFSKVKP 339

Query: 363 NGKHSANTANVKRYIDFAAAHGFDAVLVEGWNEGWEDWFGNSKDYVFDFVTPYPDFDVKE 422
           NGKH+ANTA+VK YIDFAA HGFDAVLVEGWN GWEDWFG+SKDYVFDFVTPYPDFDVK 
Sbjct: 340 NGKHAANTAHVKEYIDFAAKHGFDAVLVEGWNVGWEDWFGHSKDYVFDFVTPYPDFDVKG 399

Query: 423 IHRYAARKGIKMMMHHETSASVRNYERHMDKAYQFMADNGYNSVKSGYVGNIIPRGEHHY 482
           I  YA  KG+KM+MHHETS+SVRNYERHMD AYQFM DNGY++VKSGYVGNI+PRGE+HY
Sbjct: 400 IRDYAKSKGVKMIMHHETSSSVRNYERHMDAAYQFMKDNGYDAVKSGYVGNILPRGENHY 459

Query: 483 GQWMNNHYLYAVKKAADYKIMVNAHEATRPTGICRTYPNLIGNESARGTEYESFGGNKVY 542
            QW+ NHY YA++KAA+YKIMVNAHEA RPTGICRTYPNLIGNESARGTEY++FGG+K  
Sbjct: 460 SQWIVNHYQYALEKAAEYKIMVNAHEAVRPTGICRTYPNLIGNESARGTEYQAFGGSKPN 519

Query: 543 HTTILPFTRLVGGPMDYTPGIFETHCNKMNPANNSQVRSTIARQLALYVTMYSPLQMAAD 602
           H  +LPFTRL+GGPMDYTPGIFE   +K +P NNS V ST+A QLALYVTMYSPLQMAAD
Sbjct: 520 HVAMLPFTRLIGGPMDYTPGIFEMEISKFSPNNNSHVNSTLANQLALYVTMYSPLQMAAD 579

Query: 603 IPENYERFMDAFQFIKDVALDWDETNYLEAEPGEYITIARKAKDTDDWYVGCTAGENGHT 662
           +PE+Y +F+DAFQFIKDV ++WD++ Y+EAEP EYIT ARK K T++W+VG   G    T
Sbjct: 580 LPEHYNQFLDAFQFIKDVPVEWDDSKYIEAEPAEYITAARKEKGTNNWFVGSVGGYEART 639

Query: 663 SKLVFDFLTPGKQYIATVYADAKDADWKENPQAYTIKKGILTNKSKLNLHAANGGGYAIS 722
           S +  DFL  GK YIATVYADA +A +K NPQAYTIKKGI+T+K+KL+   A GGGYAIS
Sbjct: 640 STIKLDFLDKGKTYIATVYADANNAHYKTNPQAYTIKKGIVTSKTKLSQFVAPGGGYAIS 699

Query: 723 IKEVKDKSEAKGLKRL 738
           I E   K+E KGLK+L
Sbjct: 700 IIEA-TKAETKGLKKL 714


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: 1883
Number of extensions: 91
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: 714
Length adjustment: 40
Effective length of query: 698
Effective length of database: 674
Effective search space:   470452
Effective search space used:   470452
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 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 2024 update 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