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 (BT0339;BT_0339) (EC 3.2.1.20) (characterized)
to candidate WP_035132129.1 Q763_RS05920 alpha-xylosidase

Query= CAZy::AAO75446.1
         (748 letters)



>NCBI__GCF_000769915.1:WP_035132129.1
          Length = 798

 Score =  406 bits (1044), Expect = e-117
 Identities = 224/557 (40%), Positives = 304/557 (54%), Gaps = 26/557 (4%)

Query: 178 LPIAFCKRTGKKERATLS-FESRPDECFAGTGERFFKMDLSGQTLFLKNQDGQGVNNRRT 236
           LP ++ +R     R+    F   PDE   G GE F + +  GQ + L   D  GV N   
Sbjct: 203 LPYSYVRRNSDYSRSVAPVFSLEPDEKIFGCGESFTQFNKRGQKVVLWTDDANGVQNETM 262

Query: 237 YKNIPFYLSSRMYGTFYHTCAHSKLSLAGHSTRSVQFLSDQAMLDAFVIAGDTMEEILRG 296
           YK IPFY+SSR YG F HT     +    +   + + +    + D F+  G+  ++IL  
Sbjct: 263 YKPIPFYMSSRGYGVFMHTSTPVTVDFGKYFAGANKMMIGDDVADLFIFIGEP-KDILDE 321

Query: 297 YRDLTGYPSMPPLWSFGVWMSRMTYFSADEVNEICDRMRAEHYPCDVIHLDTGWFRTDWL 356
           Y DLTG  SMPPLWSFG WMSR+TYFS  E  EI   +R    P DVIH DTGWF  DW 
Sbjct: 322 YTDLTGKASMPPLWSFGFWMSRITYFSEKEGREIAKNLRKNKIPSDVIHFDTGWFDVDWR 381

Query: 357 CEWKFNEERFPDPKGFIQRLKKNGYRVSLWQLPYVAEDAEQIEEAKANEYIAPLTKQQDT 416
             ++F  ERF  P   +  +KK+G+ V LWQLPY             NE +      +D 
Sbjct: 382 NNYEFASERFDAPTKMMADMKKDGFNVCLWQLPYFTP-----RNTLFNEIVDNGLAVKDR 436

Query: 417 DGSNFSALDYAGTIDFTYPKATEWYKGLLKQLLDMGVTCIKTDFGENIHMDAVY-KGMKP 475
            G N    D    +DF+ P+  +WY+  LK L+D GV   K DFGE    + +Y  G   
Sbjct: 437 KG-NIPYED--AVLDFSNPETVKWYQAKLKHLMDQGVAVFKVDFGEAAPAEGIYHSGRTG 493

Query: 476 ELLNNLYALLYQKAAYEITKEVTGDGIVWARAAWAGCQRYPLHWGGDSCSSWDGMAGSLK 535
              +NLY L Y KA  E+T+   G  ++WAR+ WAG QRYPLHWGGD+ ++   M+ +L+
Sbjct: 494 FYEHNLYPLRYNKAVAELTQREKGYTLIWARSTWAGSQRYPLHWGGDAATTNGAMSATLR 553

Query: 536 GGLHFGLSGFAFWSHDVPGFHTLPNFMNSIVAEDVYMRWTQFGVFTSHIRYHGTNKREPW 595
           GGL  GL GF+FWSHDV GF T          E++Y RWT FG+ TSH+R HG    EPW
Sbjct: 554 GGLSLGLCGFSFWSHDVGGFVTKS-------PEELYKRWTPFGMLTSHVRSHGEPPTEPW 606

Query: 596 HYPA-IAPLVKKWWKLRYSLIPYIIEQSKLAVESGWPLLQALILHHPEDKLCWHIDDEYY 654
            Y        +    +RY L+PYI  Q+K + E G P+++AL + +P+D   W ID+EY 
Sbjct: 607 LYSEDFLKSFRNADNMRYELMPYIYAQAKESSEKGLPMMRALFVEYPQDAGSWLIDNEYL 666

Query: 655 FGNDFLVAPVMNSENRRDIYLPEGQWVNFFTGERLQGGRWLKEVYVPLEEMP--VYVREN 712
           FG+D LVAP+      RD+YLP GQWV++ T +++  G W +   +   E+P  V V+  
Sbjct: 667 FGSDMLVAPLFEEVTERDVYLPPGQWVDYQT-KKVYNGGWHR---IAAGELPIIVLVKSG 722

Query: 713 AVIPIYPEEVNCTDEMD 729
             IP + +    T +MD
Sbjct: 723 TAIP-HIKLAQSTKDMD 738


Lambda     K      H
   0.322    0.139    0.449 

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: 1688
Number of extensions: 88
Number of successful extensions: 6
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: 748
Length of database: 798
Length adjustment: 41
Effective length of query: 707
Effective length of database: 757
Effective search space:   535199
Effective search space used:   535199
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 (21.9 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