GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Sinorhizobium meliloti 1021

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate SM_b20891 SM_b20891 dehydrogenase

Query= metacyc::MONOMER-15203
         (503 letters)



>FitnessBrowser__Smeli:SM_b20891
          Length = 477

 Score =  280 bits (717), Expect = 6e-80
 Identities = 172/459 (37%), Positives = 239/459 (52%), Gaps = 11/459 (2%)

Query: 27  NPA-TGQVTGQVALASQADVDSAVAAAQAAFPAWSDTPPIRRARVMFKFLELLNAHKDEL 85
           NP+ T  V G+ A AS  D  +A+AAA+AAFPAWS +  + R  ++ K  + + A KDEL
Sbjct: 22  NPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEILARKDEL 81

Query: 86  AEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLKGDYTEQVSTGIDNWTTRQPLGVV 145
              ++RE GK   +  GE  R   I EF  G    L G+    V  GI    TR+P GVV
Sbjct: 82  GRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSVRPGIGVEITREPAGVV 141

Query: 146 AGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPSASLMMADLLKQAGLPDGVFNVVQ 205
             ITP+NFP+ +P W    A+  GN+ V KP+ L P  S  + D+L +AGLP GV N+V 
Sbjct: 142 GIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPKGVLNLVM 201

Query: 206 GDKDSV--EALIDHPDVKALSFVGSTPIANLIYERGARSGKRIQALGGAKNHMVVMPDAN 263
           G K SV  +A++D PDV+A++F GST     +        ++ Q   G KN  VV+ DA+
Sbjct: 202 G-KGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGKNPFVVLDDAD 260

Query: 264 LDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPRLAERARDLKIKNGLELDAEMG 323
           L  AV+A + +A+ S G+RC A S  ++   + D+ V  + ER + L + + L+    +G
Sbjct: 261 LSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVDDALKPGTHIG 320

Query: 324 PIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGEGCADGFWMGGTLFDHVTPEMT 383
           P+V      + T YI  G  EGA++   G              GF++   LF   T EM 
Sbjct: 321 PVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRD------TPGFYLQPALFTEATNEMR 374

Query: 384 IYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFTESGSVAREFGRRIQVGMVGIN 443
           I REEIFGPV A +RV D   A+ + ND  FG      T S   A  F R  + GMV +N
Sbjct: 375 ISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGMVMVN 434

Query: 444 VPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKS 482
           +P         FGG K S +G     G+    FYT  K+
Sbjct: 435 LPTAGVDFHVPFGGRKASSYG-PREQGKYAAEFYTNVKT 472


Lambda     K      H
   0.319    0.136    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: 593
Number of extensions: 26
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: 503
Length of database: 477
Length adjustment: 34
Effective length of query: 469
Effective length of database: 443
Effective search space:   207767
Effective search space used:   207767
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