GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Sinorhizobium meliloti 1021

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate SMc02689 SMc02689 aldehyde dehydrogenase

Query= SwissProt::A1B4L2
         (508 letters)



>lcl|FitnessBrowser__Smeli:SMc02689 SMc02689 aldehyde dehydrogenase
          Length = 502

 Score =  856 bits (2211), Expect = 0.0
 Identities = 411/493 (83%), Positives = 452/493 (91%)

Query: 16  PFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWG 75
           P++++Y NFIGGEW  PV+GRYF NTTPITG  + ++ARS+A DIE+ALDAAHAA+EKWG
Sbjct: 10  PYKQKYGNFIGGEWREPVAGRYFDNTTPITGGTLCEVARSDAADIEIALDAAHAAREKWG 69

Query: 76  ATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLR 135
            TS  ER+NI++KIA RME NLELLA AETWDNGKPIRETMAAD+PLAIDHFRYFA  +R
Sbjct: 70  RTSTTERSNILMKIAARMEDNLELLARAETWDNGKPIRETMAADIPLAIDHFRYFAACIR 129

Query: 136 AQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQT 195
           AQEGSI +ID DTVAYHFHEPLGVVGQIIPWNFP+LMA WKLAPA+AAGNCVVLKPAEQT
Sbjct: 130 AQEGSIGEIDHDTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQT 189

Query: 196 PAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYAS 255
           P  I+VWA LIGDLLPPGVLNIVNGFGLEAGKPLA+S RIAKIAFTGETTTGRLIMQYAS
Sbjct: 190 PGSILVWAELIGDLLPPGVLNIVNGFGLEAGKPLATSPRIAKIAFTGETTTGRLIMQYAS 249

Query: 256 ENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESI 315
           +NLIPVTLELGGKSPNIFFADVA EDDDFFDKALEGF MFALNQGEVCTCPSR L+QESI
Sbjct: 250 QNLIPVTLELGGKSPNIFFADVASEDDDFFDKALEGFAMFALNQGEVCTCPSRALVQESI 309

Query: 316 YDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAA 375
           YD+FMERAV+RV+AI+QG+P +  TMIGAQASSEQ EKIL+Y++IGK+EGAEVLTGG   
Sbjct: 310 YDRFMERAVKRVEAIRQGNPLDEATMIGAQASSEQLEKILAYIEIGKEEGAEVLTGGGRN 369

Query: 376 DLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAG 435
            L G+LSGGYY++PT+F G+N+MRIFQEEIFGPVVSVTTFK +AEALEIANDTLYGLGAG
Sbjct: 370 VLEGDLSGGYYVKPTVFHGHNRMRIFQEEIFGPVVSVTTFKTEAEALEIANDTLYGLGAG 429

Query: 436 VWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 495
           VWSRDAN CYR GR I+AGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN
Sbjct: 430 VWSRDANRCYRFGRAIEAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 489

Query: 496 MLVSYSPKKLGFF 508
           MLVSYSPK LGFF
Sbjct: 490 MLVSYSPKALGFF 502


Lambda     K      H
   0.319    0.136    0.411 

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: 951
Number of extensions: 26
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: 508
Length of database: 502
Length adjustment: 34
Effective length of query: 474
Effective length of database: 468
Effective search space:   221832
Effective search space used:   221832
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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