Alignments for a candidate for susB in Sphingomonas koreensis DSMZ 15582

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Sphingomonas koreensis DSMZ 15582

Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate Ga0059261_1579 Ga0059261_1579 Glycosyl-hydrolase 97 N-terminal/Glycosyl-hydrolase 97 C-terminal, oligomerisation/Glycoside hydrolase 97

Query= CAZy::AEW20125.1
         (708 letters)



>FitnessBrowser__Korea:Ga0059261_1579
          Length = 685

 Score =  530 bits (1366), Expect = e-155
 Identities = 298/689 (43%), Positives = 403/689 (58%), Gaps = 63/689 (9%)

Query: 31  SPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLG-LEIEGFSLRKAFTLKGVETVTFD 89
           SPDG L +   V+G+G P Y +    KP+I+PSRLG L  +   L + F ++   T + D
Sbjct: 38  SPDGKLRVTVTVDGDGRPHYAVARNGKPLIEPSRLGFLLTDAPKLERRFAIESQATSSAD 97

Query: 90  ETWTPVWGEVKAIRNHYNEMTATLHQADG-DRTMVIRFRLYDDGLGFRYEFPQQKSLNYF 148
            TW   WGE K IR+ + E    L ++    R M + FR++D+G+GFRYEFP Q +L + 
Sbjct: 98  STWEQPWGEWKTIRDRHTEFRVRLKESTALARVMDVVFRIFDEGVGFRYEFPDQPNLKHA 157

Query: 149 VIKEEYSEFAMAGDHKAFWIP-GDYDTQEYDYTESRLTEIRGLMQTAITPNTSQTPFSPT 207
            I +E +EF +AG+  A+WIP G+++  EY Y  + ++E+ G   T IT           
Sbjct: 158 NIADELTEFGLAGNGTAWWIPAGEWNRYEYLYNRTPISEV-GQAHTPIT----------- 205

Query: 208 GVQTALMMKSDDGLYINLHEAALVDYPCMSLNLDDQTLTFQSWLTPDAQGKKGYMQTPCH 267
                  +K +DG ++  HEAALVDY  M L     T  F++ L+P A   K   Q P  
Sbjct: 206 -------VKLEDGTHVAFHEAALVDYSGMWLRRVTGT-RFKAQLSPGAGPAKVVKQGPFT 257

Query: 268 TPWRTVIVSDDARRILA-SHLTLNLNEPCKLDDVSWIRPVKYIGVWWEMISGKSTWAYTN 326
           TPWRT++++DDA  +   S +TLNLNEP KL DVSW++P K++GVWW MI GK +WA   
Sbjct: 258 TPWRTMVIADDAAGLYTGSRMTLNLNEPNKLGDVSWVKPGKFVGVWWNMIKGKWSWAR-- 315

Query: 327 DLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGFDQVLVEGWNIGWE-DWFGNS 385
                               H A    V+RYIDFA  +G   VLVEGWN+GW+ DWFGN 
Sbjct: 316 -----------------GPQHGATTANVKRYIDFAGANGIPGVLVEGWNVGWDGDWFGNG 358

Query: 386 KDYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSVRNYERQMEKAYKLMNDYGYN 445
            +   +F  P  DFD KAL  YA SKG  L+ HHET  S  +Y++Q++ A+     +G  
Sbjct: 359 TE--MNFSGPTEDFDAKALAAYARSKGTALVGHHETGGSASHYDKQLDTAFAWSAAHGQK 416

Query: 446 AVKSGYV------GNIIPRG----EYHYGQWMVNHYLYAVKKAAEHRIMVNAHEAVRPTG 495
            VK+GYV      G + P G    E+H GQWM NH+L  V  AA H+I V+ HE ++ TG
Sbjct: 417 VVKTGYVADAGQIGRVDPDGSEHREWHDGQWMSNHHLRVVLAAARHKISVDPHEPIKDTG 476

Query: 496 LCRTYPNLIGNEAARGGEYESFGG-NKVFHTTILPFTRLMGGPMDYTPGIFETRLEKVNP 554
           L RTYPN +  E ARG EY ++ G N   H   L FTR++ GPMD+TPGI   + EK   
Sbjct: 477 LRRTYPNWLAREGARGQEYMAWQGKNPPEHEANLVFTRMLSGPMDFTPGILSLKGEK--- 533

Query: 555 GNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFMDAFQFIKDVAIDWDDSKYLEAE 614
             +S + ST+A+QLA YV +YSP+QMAAD PE Y + MDAFQFIKDV +DW D++ L  E
Sbjct: 534 --DSDIPSTIAKQLAQYVVIYSPVQMAADEPEVYAKLMDAFQFIKDVPVDWADTRILNGE 591

Query: 615 PGRYITVARKAKGTNNWFVGCTANEDGHLSNVSLDFLDPGRKYTATIYADAPTAHYEKNP 674
            G Y+T+ARK +   +W++G   +E      V+LDFLDPG+ YTA IY DAP   ++ + 
Sbjct: 592 VGDYVTIARKDRNGADWYLGSVGDEQARNLEVTLDFLDPGKTYTAQIYRDAPDTRFDSDT 651

Query: 675 Q-AYTIKQMKVTNKSKLTLRAASGGGYAI 702
           +  Y I+  KV    KL L  A GGG AI
Sbjct: 652 RHKYVIETRKVKRGDKLMLALAPGGGQAI 680


Lambda     K      H
   0.319    0.135    0.417 

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: 1439
Number of extensions: 91
Number of successful extensions: 12
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: 708
Length of database: 685
Length adjustment: 39
Effective length of query: 669
Effective length of database: 646
Effective search space:   432174
Effective search space used:   432174
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 (21.7 bits)
S2: 54 (25.4 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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