GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Phaeobacter inhibens BS107

Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF3742 PGA1_262p01460 aldehyde dehydrogenase

Query= reanno::WCS417:GFF827
         (481 letters)



>FitnessBrowser__Phaeo:GFF3742
          Length = 497

 Score =  518 bits (1333), Expect = e-151
 Identities = 254/473 (53%), Positives = 339/473 (71%)

Query: 9   NYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQARH 68
           N I G+W+AG     N NPS+LSD++G +A+A   Q+ A +D A+ A   W+  G++ + 
Sbjct: 22  NLIAGEWLAGESEVENRNPSDLSDLVGIFAQASADQLEATLDQAQVAQREWAAYGLERKQ 81

Query: 69  DALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPS 128
             L+ +G+E++AR EELGTLL+REEGK L E  GEV RAG  F ++A ECLR  G+   S
Sbjct: 82  AVLNAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAECLRQIGENADS 141

Query: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALA 188
           VRP + V+V REA+G V +I+PWNFP A  +WKIAPAL YGN VV KPA + P  A ALA
Sbjct: 142 VRPDIEVDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANITPASAVALA 201

Query: 189 EIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ 248
           EII R   P G+F+LVMGSGR +G  LV SPKV+ ISFTGSV VG+ IA + +    KVQ
Sbjct: 202 EIIERQDIPKGLFSLVMGSGRSIGQRLVESPKVNAISFTGSVPVGKGIASAAIQNLTKVQ 261

Query: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMAERM 308
           +EMG KN   ++DDADL  AV L++  AF  TGQ+CTASSRL+V AGIHD FV  +    
Sbjct: 262 MEMGSKNALAVMDDADLDLAVTLALGGAFGGTGQKCTASSRLVVHAGIHDAFVEKLVTGA 321

Query: 309 KSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYLAPT 368
           K++KVGHAL++G  +GPVVS+ QL+++L Y+D+G++EGA L  GG  +    +G+Y++P 
Sbjct: 322 KAMKVGHALEAGVQMGPVVSEQQLNENLAYVDLGKTEGAELACGGQRLEMPHQGFYMSPG 381

Query: 369 LFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKR 428
           +F ++   MRI+REE+F P+ +V++V  Y+ AL++ NDT FGL++GI T SL  A HF+R
Sbjct: 382 VFLNTTNDMRINREEMFAPLTSVIKVGSYDEALSVVNDTNFGLTSGIVTQSLARATHFRR 441

Query: 429 HSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIGS 481
           +++ G+V VNLPTAG DYHVPFGGR  SSYG REQG+ A EFYT VKT+YI +
Sbjct: 442 NARTGVVTVNLPTAGTDYHVPFGGRGDSSYGPREQGKAAAEFYTTVKTAYISA 494


Lambda     K      H
   0.318    0.134    0.390 

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: 571
Number of extensions: 13
Number of successful extensions: 1
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: 481
Length of database: 497
Length adjustment: 34
Effective length of query: 447
Effective length of database: 463
Effective search space:   206961
Effective search space used:   206961
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