Alignments for a candidate for lacZ in Saccharomonospora cyanea NA-134

GapMind for catabolism of small carbon sources

Alignments for a candidate for lacZ in Saccharomonospora cyanea NA-134

Align Exo-alpha-(1->6)-L-arabinopyranosidase; APY; Beta-D-galactopyranosidase; EC 3.2.1.- (characterized)
to candidate WP_005457463.1 SACCYDRAFT_RS15370 beta-glucosidase

Query= SwissProt::E7CY69
         (757 letters)



>NCBI__GCF_000244975.1:WP_005457463.1
          Length = 772

 Score =  232 bits (591), Expect = 6e-65
 Identities = 193/654 (29%), Positives = 302/654 (46%), Gaps = 71/654 (10%)

Query: 68  ATCFPPAAGLSSSWNPELIHKVGEAMAEECIQEKVAVILGPGVNIKRNPLGGRCFEYWSE 127
           AT +P     +++++PEL+ ++  A+  +     V   L P +++ R+   GR  E   E
Sbjct: 122 ATVYPAPLAWAATFDPELVERMAAAIGADMRAVGVHQGLSPVLDVARDHRWGRVEETLGE 181

Query: 128 DPYLAGHEAIGIVEGVQSKGVGTSLKHFAANN-QETDRLRVDARISPRALREIYFPAFEH 186
           DPYL G      V G+QS+GV  +LKHFA  +     R      I PR LR++  P FE 
Sbjct: 182 DPYLVGMLGSAYVRGLQSEGVIATLKHFAGYSASRAARNHAPVPIGPRELRDVILPPFEM 241

Query: 187 IVKKAQPWTIMCSYNRINGVHSAQNHWLLTDVLRDEWGFDGIVMSDW------------- 233
            V+ A   ++M +Y  ++GV +A +  LLT VLRDEWGF+G V+SD+             
Sbjct: 242 AVRDAGAGSVMNAYVDLDGVPAAADATLLTGVLRDEWGFEGTVVSDYWAVAFLATMHRVA 301

Query: 234 -GADHDRGASLNAGLNLEMPPSYT-DDQIVYAVRDGLITPAQLDRMAQGMI--------- 282
            GA      +L AG+++E+P +     ++V  VR G +  A +DR A  ++         
Sbjct: 302 DGAADAGALALAAGIDVELPDALCYGAELVERVRRGEVDEALVDRAAMRVLRQKAELGLL 361

Query: 283 --DLVNKTRAAMSIDNYRFDVDAHDEVAHQAAIESIVMLKNDDAILPLNA--------GP 332
             D   ++    S+D    D  AH E+A + A  S+V+L N D +LPL A        GP
Sbjct: 362 DPDWTPESDVDSSVD---LDAGAHRELARRIAERSVVLLAN-DGVLPLAAEHRRIALVGP 417

Query: 333 VANPSATPQKIAVIGEFAR----TPRYQGGGSSHITPTKMTSFLDTLAERGIKADFAPGF 388
            A+       +A +G ++      PRY G G     P+ + +    L +  I A   PG 
Sbjct: 418 CAD-----DPLAFLGCYSYPNHVLPRYPGLGLGIEVPSLVEALRAELPDAEITA--VPG- 469

Query: 389 TLDLEPADPALESEAVETAKNADVVLMFLG-----LPEAVESEGFDRDTLDMPAKQIALL 443
              +   D +  +EAV  A  ADV +  +G       E    EG D   L +P  Q  LL
Sbjct: 470 -CGVNDDDRSRFAEAVTAADGADVCVAVVGDRAGLFGEGTSGEGCDAPDLRLPGVQEELL 528

Query: 444 EQVAAANQNVVVVLSNGSVITVAPWAKNAKGILESWLLGQSGGPALADVIFGQVSPSGKL 503
             + A    VVVV+ +G    +   A +A  +++++L G+ GG ALA ++ G+ +PSG+L
Sbjct: 529 SALLATGTPVVVVVVSGRPYALGAHADHAAAVVQAFLPGEEGGAALASILSGRTAPSGRL 588

Query: 504 AQSIPLDINDDPSMLNWPGEEGHVDYGEGVFAGYRYYDTYGKAVDYPFGYGLSYATFEIT 563
              +P      P+    P   G+    +G+               +PFG+GLSY TF+  
Sbjct: 589 PVQVPRHPGGQPATYLHPPLGGN---SQGI-------SNLDPTPAFPFGHGLSYTTFDYG 638

Query: 564 GVAVAKTGA---NTATVTATVTNTSDVDAAETVQVYVVPGKADVARPKHELKGFTKAFLK 620
           G+ V+        T  +   V N+ +   +E VQ+Y+   +A V RP  +L GF +  L 
Sbjct: 639 GLTVSAEQVPTDGTLDIAVDVRNSGERAGSEVVQLYLDDVQAQVTRPVRQLAGFARVDLA 698

Query: 621 AGESKTVAIDLDERAFAYWSEKYNDWHVEAGEYAIEVGVSSRDIADTVAVALDG 674
            GE+  V   L     ++         VE G   + VG S  D+  + +  L G
Sbjct: 699 PGETARVTFTLHADRTSFTGRDLGR-IVEPGRIDVHVGRSVADLPCSASFELTG 751


Lambda     K      H
   0.315    0.132    0.393 

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: 1380
Number of extensions: 78
Number of successful extensions: 8
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: 757
Length of database: 772
Length adjustment: 40
Effective length of query: 717
Effective length of database: 732
Effective search space:   524844
Effective search space used:   524844
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: 42 (22.0 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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Protein sequences (fasta format)
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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