GapMind for catabolism of small carbon sources

 

Alignments for a candidate for susB in Shewanella amazonensis SB2B

Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate 6936934 Sama_1108 alpha-glucosidase (RefSeq)

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



>FitnessBrowser__SB2B:6936934
          Length = 676

 Score =  498 bits (1283), Expect = e-145
 Identities = 285/714 (39%), Positives = 399/714 (55%), Gaps = 69/714 (9%)

Query: 13  LFSFLVSAPFTMRAEELKSPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLGLEI-EG 71
           L +   S P   +   LKSP+G + +R  V+ +  P Y + +  KPVI  S+LG +    
Sbjct: 7   LLAMAASLPLQAKTLSLKSPNGEIELR--VSDDDAPHYAVLFHGKPVIGASKLGFDFTNA 64

Query: 72  FSLRKAFTLKGVETVTFDETWTPVWGEVKAIRNHYNEMTATLHQADGDRTMVIRFRLYDD 131
            + R  F +   +  T D +W   WGE + I + +NE+  +    D  +   +RFR +DD
Sbjct: 65  ANFRGGFDITDSQRATVDSSWEQPWGEARIIEDKHNELVVSFTHPDSKQAYKVRFRAFDD 124

Query: 132 GLGFRYEFPQQKSLNYFVIKEEYSEFAM--AGDHKAFWIPG-DYDTQEYDYTESRLTEIR 188
           G+GFRYE      LN   I  E +EFA+  A   +A+WIPG  ++  EY Y  S+L +  
Sbjct: 125 GVGFRYEVNANTPLN---IGRELTEFAIEDADKAEAWWIPGRGWNRYEYLYQHSKLADAA 181

Query: 189 GLMQTAITPNTSQTPFSPTGVQTALMMKSDDGLYINLHEAALVDYPCMSLNLDDQTLTFQ 248
            +          QTPF+         +K+ DG++I +HEAALVDY  M+LN   +  TF 
Sbjct: 182 LV----------QTPFT---------LKNKDGVHIAIHEAALVDYAAMTLN-QRRPGTFV 221

Query: 249 SWLTPDAQGKKGYMQTPCHTPWRTVIVSDDARRILASHLTLNLNEPCKLDDVSWIRPVKY 308
           + LTP + G         +TPWRT+ ++ +A  ++ SHL LNLNEP +L DVSW+ P KY
Sbjct: 222 AELTPWSDGVAVKTNGTFNTPWRTLHIAPNATGLINSHLILNLNEPNQLGDVSWVEPGKY 281

Query: 309 IGVWWEMISGKSTWAYTNDLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGFDQ 368
           +G+WW M   K+TW                        H A   + ++Y+ FAA +GFD 
Sbjct: 282 VGIWWGMHINKNTWG-------------------SGSQHGATTAETKKYLRFAADNGFDG 322

Query: 369 VLVEGWNIGWE-DWFGNSKDYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSVRN 427
           VLVEGWNIGW+ DWF N    +F F  P+ DFD+KA+ +Y    G +L+ HHETS SV N
Sbjct: 323 VLVEGWNIGWDGDWFHNGD--LFSFTKPFADFDIKAIADYGREVGARLIGHHETSGSVSN 380

Query: 428 YERQMEKAYKLMNDYGYNAVKSGYV---GNI-------IPRGEYHYGQWMVNHYLYAVKK 477
           Y +Q + A+ L    G   VK+GYV   GNI       + R E+H GQ+MV  YL  VK 
Sbjct: 381 YRKQWDGAFSLYQKMGVAQVKTGYVADGGNIKRIDENGLERFEWHDGQFMVGEYLDNVKT 440

Query: 478 AAEHRIMVNAHEAVRPTGLCRTYPNLIGNEAARGGEYESFGG--NKVFHTTILPFTRLMG 535
           AA+++I +N HE ++ TGL RTYPN +  E ARG EY ++G   N   H  +L FTR++ 
Sbjct: 441 AAKYQISINTHEPIKDTGLRRTYPNWLAREGARGQEYNAWGNPPNPPEHIAMLSFTRMLA 500

Query: 536 GPMDYTPGIFETRLEKVNPGNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFMDAF 595
           GPMD+TPGIF+     +    N    STLA+QLALYV +YSP+QMAADLPENY +  DAF
Sbjct: 501 GPMDFTPGIFDMSFNGLGDNTNR-PQSTLAKQLALYVVLYSPIQMAADLPENYLKRPDAF 559

Query: 596 QFIKDVAIDWDDSKYLEAEPGRYITVARKAK-----GTNNWFVGCTANEDGHLSNVSLDF 650
           QFIKDV  DW+ S  L+   G ++ +ARK +       N+W++G   +E+     V LDF
Sbjct: 560 QFIKDVPTDWEQSIALDGAVGDFVVMARKERKARQYSGNDWYLGAVTDENARDVTVKLDF 619

Query: 651 LDPGRKYTATIYADAPTAHYEKNPQAYTIKQMKVTNKSKLTLRAASGGGYAISI 704
           L+PG+ + A IY D   A ++  P    IK+  V     L+L  A GGG A+ +
Sbjct: 620 LEPGKTFEAQIYQDGKDAEWKWRPYEMDIKKQTVRKGDTLSLHLAEGGGAAVRL 673


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: 1437
Number of extensions: 72
Number of successful extensions: 11
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 708
Length of database: 676
Length adjustment: 39
Effective length of query: 669
Effective length of database: 637
Effective search space:   426153
Effective search space used:   426153
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.

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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:

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