Alignments for a candidate for bgl in Synechococcus elongatus PCC 7942

GapMind for catabolism of small carbon sources

Alignments for a candidate for bgl in Synechococcus elongatus PCC 7942

Align β-glucosidase (TxGH116;Thexy_2211) (EC 3.2.1.21) (characterized)
to candidate Synpcc7942_0854 Synpcc7942_0854 hypothetical protein

Query= CAZy::AEF18218.1
         (806 letters)



>FitnessBrowser__SynE:Synpcc7942_0854
          Length = 798

 Score =  559 bits (1441), Expect = e-163
 Identities = 301/800 (37%), Positives = 451/800 (56%), Gaps = 58/800 (7%)

Query: 38  DIPDSAWTIGIGEKFKNAGHPNVKYPM-IDDSYVQGAPLGGFGAGTIGRTYNGGFSRWHL 96
           ++P +AW   +G  ++      V+Y   +DD    GAPLGGFGAG  GR+  G  + WHL
Sbjct: 4   ELPAAAWRRPLGLGWEKPY--TVRYASNLDDGPWHGAPLGGFGAGCWGRSPRGDVTLWHL 61

Query: 97  EIGKNKYTTVYANQFSVFQKVEGNKDGVAQVLYAGEPENGYLSSWKWDYP-----KESGM 151
           + G++ Y ++ A QF+V++   G     A  L    P +G LSSW W YP     + +G 
Sbjct: 62  DGGEHWYGSIPACQFAVYESGTG-----AYALSTEAPSDGSLSSWNW-YPASTAERSTGE 115

Query: 152 YYALYPNSWYTYTNKDLPVQLAVKQFSPIIPYNYKETSYPVAVFKWTAYNPTNKNVDVSI 211
           Y ALYP S ++Y  +    ++  +QFSPI+P++Y+ TSYP A+F+W  +NP+++ + +SI
Sbjct: 116 YSALYPRSQFSY-QQVFEAEIHCRQFSPILPHDYQATSYPTAIFRWQLHNPSDRPLTISI 174

Query: 212 MFTWQNMIGFFGKQVNVNSGNFNKIIKDKSKDSEIVAAV---MGNI-------------- 254
           + +W+N+ G+F    N N         D S   + V A+   +GN+              
Sbjct: 175 LLSWENLCGWF---TNTNKAPEVVYRDDGSPVYDYVPALGQSVGNLNQRIAGEGWQGLLL 231

Query: 255 ----SNDNEEWNGEYSIGVKKVPGVDISYKAKFVTTGDGSDLWHEFSKNGILDNKDDETP 310
               S D EE +G+++I + +  G++I    ++  TGDGS+LW  F+ +G + ++ D  P
Sbjct: 232 DQTRSQDPEEGDGQWAIAIAEAEGLEIFRCDRWDPTGDGSELWQSFALDGSIPDRQDSQP 291

Query: 311 TKQ-DGIGSAIAVNFKLQPGQTIEVPFALSWDLPIMKFGGGDKWYKMYTKYFGKNGKNSF 369
               + +  AIAV   LQPG++ E+PF+++WDLP+ +F  G K ++ YT +FG++G+N+ 
Sbjct: 292 AAAGERLAGAIAVRLTLQPGESREIPFSIAWDLPVTEFAAGVKAFRRYTDFFGRDGRNAA 351

Query: 370 AILKEALNNYQKWEKMIDDWQKPILSNKSKPDWYKTALFNELYYLADGGTAWENGKVGEK 429
           AI    L +Y +WE+ I  WQ+PIL      D +K  LFNELY L  GG+ W        
Sbjct: 352 AIAATGLKHYDEWEQAIAAWQQPILDRDDLSDTFKLGLFNELYDLCSGGSLW----TAAS 407

Query: 430 DKRTNNMFGLLECFDYNYYETLDVRFYGSFPLVMLWPDIEKQVMRQFADTINVQDSSE-- 487
           +      F +LEC DY +YE+LDVR YG+F L+MLWP++EK VMR FA  I   D     
Sbjct: 408 EADPVGQFAVLECLDYAWYESLDVRLYGAFGLLMLWPELEKAVMRAFARAIPQADDRTRV 467

Query: 488 ----FKVGSNGAMAVKKVQGMIPHDLGSSYALPWIKINAYDWQNPNIWKDLNSKYVLLVY 543
               F +G    +A +K+    PHDLG+    PW++ N   +Q+ N+WKDL   +VL V+
Sbjct: 468 IGYWFTIGQESPLAKRKLANATPHDLGAPNESPWLQTNYTGYQDCNLWKDLGCDFVLQVW 527

Query: 544 RDYVLTGKTDKEFLKYTWKSVKTALDKLKEMDKDNDGIPDNEGIPDQTYDTWSMKGTSAY 603
           RDY LTG +D+ FL   W +   AL  LK+ D D DGIP+N G PDQT+D W ++G SAY
Sbjct: 528 RDYQLTGSSDRGFLSDCWPAAVAALRYLKDFDLDGDGIPENSGAPDQTFDDWRLQGISAY 587

Query: 604 CGSLWLAALKAAQEIGKVLK---DNEAYIKYNEWYKIAQQNFEKELWNGEYYNFDTESDH 660
           CG LW+AAL+AA  I  VL+   ++     +  W   A+  +   LWNG YY  D+ S  
Sbjct: 588 CGGLWIAALEAALAIADVLELSAEDRDRQDFQSWLAQARSLYHDTLWNGRYYQLDSGSG- 646

Query: 661 KDSIMADQLAGQWYADILRLGDILPKDHVQKALKKIYEFNVMKFENGKMGAVNGMRPDGI 720
              +MADQL G +Y+ +L+L  + P +  Q     +YE    KF +G+ G  NG+ PDG 
Sbjct: 647 SQVVMADQLCGDFYSRLLQLPPVAPLEAAQSTADMVYEACFQKFHSGQFGLANGLLPDGS 706

Query: 721 -VDESDIQAQEVWTGVTYALASFMKYRGMTEEAYNTAYGVYKMTYDKSGKGYWFRTPEAW 779
            VD       EVWTG+ + +A++    G  +  +     V +  YD    G  FRTPEA 
Sbjct: 707 PVDPKGTHPLEVWTGINFGIAAYWLLLGHRDRCFEVTETVIRQIYD---NGLQFRTPEAI 763

Query: 780 TKDGNYRASMYMRPLSIWSM 799
           T +  +RAS Y+RP++IW++
Sbjct: 764 TANATFRASHYLRPMAIWAV 783


Lambda     K      H
   0.316    0.135    0.422 

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: 2167
Number of extensions: 129
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: 806
Length of database: 798
Length adjustment: 41
Effective length of query: 765
Effective length of database: 757
Effective search space:   579105
Effective search space used:   579105
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 (21.6 bits)
S2: 55 (25.8 bits)

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

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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 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