GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Sphingomonas koreensis DSMZ 15582

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases

Query= reanno::WCS417:GFF2142
         (499 letters)



>FitnessBrowser__Korea:Ga0059261_1680
          Length = 469

 Score =  231 bits (588), Expect = 5e-65
 Identities = 152/460 (33%), Positives = 234/460 (50%), Gaps = 19/460 (4%)

Query: 23  VFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRARVLFEYLHLLRERKDD 82
           V +PATG       LAS   +  AVAAA+ AF GWA TP   RA  +      +   KD+
Sbjct: 21  VIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAAILAIADSIEAAKDE 80

Query: 83  LARIIVAEHGKVFTDAQGEVDRGIDILEFACGIP---NLLKGEHSDQVSRGMDNWTMRQP 139
           LAR++ AE GK   +A GE+   +       G+    ++LK + S +V         R+P
Sbjct: 81  LARLLSAEQGKPVPNAVGEIMGALAWARATAGLRPAVDVLKDDDSVRVE------VHRKP 134

Query: 140 LGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSASLFMAELLREAGLPKGVF 199
           LGVVA ++P+NFPVM+ +W     + AGNT ++KPS   P A+L M E+   A LP GV 
Sbjct: 135 LGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIAN-AHLPPGVL 193

Query: 200 NVVQGDKESVDALIEHPDVKAVSFVGSTPIAQYIYETGARNGKRVQGLGGAKNHMVVMPD 259
           N V G+ E   A+  HP +  + F GSTP  + I   GA N KR+    G  +  +V+PD
Sbjct: 194 NSVTGEVEIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTLELGGNDAAIVLPD 253

Query: 260 ADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAALTERAKHLRITDGRDLKAE 319
           AD++K    +   A+G++G+ C A+    +   + D +   L E A+   +  G D  ++
Sbjct: 254 ADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMARTAVVGPGSDAASQ 313

Query: 320 MGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEPGLENGFWLGATLFDHVTEEMS 379
            GP+ +R   + +    +     G + L  G      E    +G++   ++   VT+ M 
Sbjct: 314 FGPVQNRKQFDLVRALADDARAHGGRFLAGG------EAREGDGYFFPLSVVVDVTDGMR 367

Query: 380 IYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFTRDGNIAREFARRIEVGMVGIN 439
           I  EE FGP+L  +R +D  +A+   NA+E G G S ++ D   A  FA+R+E G V +N
Sbjct: 368 IVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAGTVWVN 427

Query: 440 VPISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFYTKQKSI 479
              S+      FGG K+S  G    +G  G+  Y + +++
Sbjct: 428 DHASISPD-VPFGGAKQSGVGT--EFGLYGLEEYMQLQTV 464


Lambda     K      H
   0.320    0.136    0.407 

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: 541
Number of extensions: 28
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: 499
Length of database: 469
Length adjustment: 34
Effective length of query: 465
Effective length of database: 435
Effective search space:   202275
Effective search space used:   202275
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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