GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mak in Desulfotomaculum hydrothermale Lam5

Align hexokinase (EC 2.7.1.1) (characterized)
to candidate WP_008410212.1 DESHY_RS02610 hexokinase

Query= BRENDA::Q09756
         (484 letters)



>NCBI__GCF_000315365.1:WP_008410212.1
          Length = 436

 Score =  211 bits (537), Expect = 4e-59
 Identities = 144/456 (31%), Positives = 237/456 (51%), Gaps = 38/456 (8%)

Query: 23  LNKTLQDHLDELEEQFTIPTELLHRVTDRFVSELYKGLTTNPGDVPMVPTWIIGTPDGNE 82
           + K L   L+++E  F + +  +  +  +  +E+  GL    G + M+PT++   P G+E
Sbjct: 1   MTKLLIQKLEQIENAFYLSSVQVRELAKKLQTEM-TGLP-GQGSLQMLPTFM-QLPAGSE 57

Query: 83  HGSYLALDLGGTNLRVCAVEVQGNGKFDIT-QSKYRLPQE-------LKVGTREALFDYI 134
            G++LA+D GGTN+R+  VE+ G G++ I  Q  +RL           +  T EALFD++
Sbjct: 58  TGTFLAVDFGGTNVRLQLVELLGRGQYAIKKQHSFRLKDPSGRYDFTARETTGEALFDFL 117

Query: 135 ADCIKKFVEEVHPGKSQNLEIGFTFSYPCVQRSINDASLVAWTKGFDIDGVEGESVGPLL 194
           A  I  F+E           +G TFS+PC Q + N A L+ WTK F    V G  +  LL
Sbjct: 118 AGQIASFMEGTFA-----TSLGLTFSFPCRQLAANKAVLLHWTKEFQTSAVVGREIMGLL 172

Query: 195 SAALKRVGCNNVRLNAILSDTTGTLVASNYASPGTEIGVIFGTGCNACYIEKFSEIPKLH 254
           + AL   G  +++  A+++DTTGTL+ + Y++P  +IG I GTG N CY +         
Sbjct: 173 AGALADRGLAHLQPAALINDTTGTLLTAAYSNPHADIGSICGTGHNTCYFK--------- 223

Query: 255 KYDFPEDMNMIINCEWCDFDNQHVVLPRTKYDVAIDEESPRPGLQTYEKMIAGCYLGDIL 314
                ++  MIIN E  +F         T YD  +D  S RPG Q  EK +AG YLG+I 
Sbjct: 224 ----TKEPAMIINMEAGNFKQ----FALTAYDRLLDSNSRRPGTQLLEKAVAGRYLGEIC 275

Query: 315 RRILLDLYEQGALFNGQDVTKIRDPLAMDTSVLSAIEVDPFENLDETQTLFEETYGL-KT 373
           R ILLD+ EQG LF G     +R    +DTS L+ +  D   +L            +  T
Sbjct: 276 RLILLDMVEQGLLFRGSIPALVRQQQTIDTSELALLAADNSPSLLHIDRWLAARQNIHPT 335

Query: 374 TEEERQFIRRACELIGTRSARLSACGVCALVRKMN---KPSMIVGTDGSVYNLYPRFKDR 430
           T  +RQ +++    + +RSARL       ++++++   +   ++G DGS++   P +  +
Sbjct: 336 TLTDRQVLKKIALTVISRSARLVGATYIGILQQIDPGLQRRHVIGLDGSLFEKMPGYLSK 395

Query: 431 LAQAFKDILGEEIGSKVVTIPAEDGSGVGAALVSAL 466
           +    +++  ++  S ++ +   +GSG+GAA+ +A+
Sbjct: 396 VRAVLREVFNDKAQS-ILPVLTGNGSGIGAAIAAAV 430


Lambda     K      H
   0.318    0.137    0.406 

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: 449
Number of extensions: 23
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: 484
Length of database: 436
Length adjustment: 33
Effective length of query: 451
Effective length of database: 403
Effective search space:   181753
Effective search space used:   181753
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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