GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Williamsia sterculiae CPCC 203464

Align α-glucosidase (AglA) (EC 3.2.1.20) (characterized)
to candidate WP_076480784.1 BW971_RS14260 DUF3459 domain-containing protein

Query= CAZy::AAA57313.1
         (544 letters)



>NCBI__GCF_900156495.1:WP_076480784.1
          Length = 538

 Score =  587 bits (1513), Expect = e-172
 Identities = 293/528 (55%), Positives = 364/528 (68%), Gaps = 13/528 (2%)

Query: 19  WWRHAVIYQIYVRSFADSNGDGEGDLNGIRERLPALVSLGVDAIWLTPFYVSPLADGGYD 78
           WW+ A+ YQIY RSFAD NGDG GDL G+ E+L  L  LG+DA+WL+P   SP+AD GYD
Sbjct: 17  WWQDAIFYQIYPRSFADGNGDGVGDLRGVAEKLGYLELLGIDALWLSPVMRSPMADHGYD 76

Query: 79  VADYRDVDPRFGTLADFDALLATAHDLGLRVIIDIVPNHTSSAHRWFRDALAAGPGSPER 138
           V+D RD+DP FG+LA  DALL  AH+ G++V +D+VPNHTS  H WF +AL + PGSPER
Sbjct: 77  VSDPRDIDPLFGSLAAMDALLVAAHERGMKVTMDLVPNHTSDQHPWFVEALNSAPGSPER 136

Query: 139 DRYVFRPGRGENGELPPNNWQSIFGGPAWTRVTEPDGTPGEWYLHLFDVEQPDLNWENPE 198
            RY+FR GRG++GELPPNNW S+FGGPAW RVTE DG+PG+WYLHLF  EQPDLNWENPE
Sbjct: 137 ARYIFRDGRGDHGELPPNNWPSVFGGPAWHRVTEADGSPGQWYLHLFAPEQPDLNWENPE 196

Query: 199 VRAEFADILRFWLDRGVDGFRIDVAHGMIKDPALPDIAEGQKADMLDGHTRLPYFDQDGV 258
           V  +    LRFWLDRGVDGFRIDVAHGM+K   LPD+ +  +  +L      P F+  GV
Sbjct: 197 VFEDLEKTLRFWLDRGVDGFRIDVAHGMVKPSDLPDM-DVSEVQLLVNRDGDPRFNNPGV 255

Query: 259 HEIYREWRAIVDSYPGERALVAEAWVENAERVARYLRPDELHQAFNFEYLTADWDAATLR 318
           H I+R  R ++D YP E   V E WVE+ +  A YLRPDELH  FNF  +   +DA  +R
Sbjct: 256 HAIHRRIRTVMDEYP-EAMTVGELWVESNDAFAEYLRPDELHLGFNFRLVKTAFDAVEIR 314

Query: 319 AVVDRSLAANNAVGAPTTWVLSNHDVTRHVTRFGGG---AQGLARARAALLLMLALPGSV 375
             ++ S+ A + VG   TW LSNHDV R VTR+  G     GL RA+A +L+ LALPG+ 
Sbjct: 315 EAIEESINAVDLVGGTPTWTLSNHDVEREVTRYADGVGPGAGLERAKAMILVELALPGTS 374

Query: 376 YLYQGEELGLPEVTDLPEEALQDPTWKRSGYTERGRDGCRVPLPWEGDEPPFGFGCSAER 435
           ++Y G ELGLP V DLP+E LQDPTW+RSG+TERGRDGCRVPLPWEG+ PPFGF  +  R
Sbjct: 375 FVYNGAELGLPNV-DLPDEVLQDPTWERSGHTERGRDGCRVPLPWEGNRPPFGFSTN-PR 432

Query: 436 SWLPVPAEWRSLTREVQERDPDSTLSLYKKALRLRRELLLPAEDALHWADAPQNVLAFRR 495
           +WLP+P EW   T E Q  +  STLSLY++A+ +R+     +   + W  AP+  LAFRR
Sbjct: 433 TWLPIPPEWADRTAEGQLENVHSTLSLYREAIEMRKTRPEFSGRGVEWYGAPEGCLAFRR 492

Query: 496 EPGF-TCAVNFGADPVTLPFEGEVVLSSGPVEQDGTHLVLPGDTAVWL 542
             G   CA+N    PV  P  GE++L S P+ QDG    L  + A WL
Sbjct: 493 SEGHAVCALNTTDTPVGFP-PGELLLCSAPL-QDGK---LAPNAAAWL 535


Lambda     K      H
   0.320    0.139    0.448 

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: 1261
Number of extensions: 72
Number of successful extensions: 7
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: 544
Length of database: 538
Length adjustment: 35
Effective length of query: 509
Effective length of database: 503
Effective search space:   256027
Effective search space used:   256027
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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:

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