GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garD in Sphingomonas koreensis DSMZ 15582

Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate Ga0059261_2974 Ga0059261_2974 Altronate dehydratase

Query= reanno::WCS417:GFF829
         (517 letters)



>FitnessBrowser__Korea:Ga0059261_2974
          Length = 490

 Score =  211 bits (536), Expect = 6e-59
 Identities = 150/463 (32%), Positives = 226/463 (48%), Gaps = 16/463 (3%)

Query: 9   SPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEGGQIIRYGQ 68
           +P ++R+H  D V   + +  + AG E   G+   D IP++HK  L     G  ++++G 
Sbjct: 2   NPAALRIHGADTVATALRN--LVAG-EVVLGVTLSDAIPRAHKFALVAHAPGDPVLKFGF 58

Query: 69  TIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGYRNADGTVG 128
            IG A A I  G  V    +    A    +         A A      + GY  ADG  G
Sbjct: 59  PIGRATAAIAPGDHVHVHNVATALAGEA-AYGGGAGAERAPAAASAIKWRGYPRADGRAG 117

Query: 129 TRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAITATDAYIP 188
           TRN + I  TV CV G     +    + LLP    VD V A  H +GC       D    
Sbjct: 118 TRNEIWILPTVGCV-GRTAQKIAVKAEALLPA--GVDGVHAFAHPFGCSQLSDDLDGTRN 174

Query: 189 IRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQDSSHGFTEM 248
           I +   LA++PN GG  L++ LGCE  Q   ++      V +    +   Q S     E 
Sbjct: 175 ILSA--LAQHPNAGG-VLLVGLGCESNQLSALLETLPEDVRMRVRTV-GAQSSPDEIGEG 230

Query: 249 IEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYASDLLLRAG 308
           + +++ LA+         +RE +    L+LG++CGGSD  SG+TANP +G  +D +  AG
Sbjct: 231 VGKVLELAQLAATA----QREEMGLDRLVLGVKCGGSDGLSGLTANPLVGIMADRITDAG 286

Query: 309 ATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSANTTPGNKKG 368
            + + +E+ E+  A  LL +RA +      +   ++ + RY        S N +PGN  G
Sbjct: 287 GSAILTEIPEIFGAEQLLMARAADADTFDAIGALVNRFKRYFIDHGEPVSENPSPGNIAG 346

Query: 369 GLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQLAAGMNLH 428
           G++ + EKSLG++ K G + +  V+  G+R K  GL     P +D V  T   AAG  + 
Sbjct: 347 GITTLEEKSLGAVQKGGQAIVTDVIDYGDRVKRTGLTLLEAPGNDAVSSTALSAAGATVI 406

Query: 429 VFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIAT 471
           +FTTGRGTP G   AP +K+++ ++LA R P  ID DAG++ T
Sbjct: 407 LFTTGRGTPLGFP-APTLKIASNSDLAARKPGWIDFDAGQVLT 448


Lambda     K      H
   0.318    0.135    0.401 

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: 661
Number of extensions: 23
Number of successful extensions: 4
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: 517
Length of database: 490
Length adjustment: 34
Effective length of query: 483
Effective length of database: 456
Effective search space:   220248
Effective search space used:   220248
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: 52 (24.6 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