Alignments for a candidate for aldA in Sinorhizobium medicae WSM419

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Sinorhizobium medicae WSM419

Align NAD⁺-dependent L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_012066669.1 SMED_RS12210 aldehyde dehydrogenase

Query= metacyc::MONOMER-16246
         (477 letters)



>NCBI__GCF_000017145.1:WP_012066669.1
          Length = 478

 Score =  588 bits (1515), Expect = e-172
 Identities = 298/471 (63%), Positives = 358/471 (76%), Gaps = 4/471 (0%)

Query: 10  NYIDGAFVES--AAHLEVFNPANGALLSRVPAASAEEVERALAAARAAQKDWARKPAIER 67
           +YIDG FVE   +  + V+NPA+   ++ +P   AE V+ A+ AAR AQ  W+  P IER
Sbjct: 6   HYIDGRFVEDRISGRIAVYNPASEEQIAEIPDGPAEVVDAAVDAARKAQPAWSELPPIER 65

Query: 68  AGHLRRIAAKIRADAGRIARTITLEQGKIASLAEVEVNFTADYLDYMAEWARRLEGEIIA 127
           AG+++ IA KIRA    +A TI+ EQGK+ SLA  EV   A  +DYMAEWARR+EGEIIA
Sbjct: 66  AGYVKAIAEKIRAKVDILAETISREQGKVVSLARGEVLGMAGLMDYMAEWARRIEGEIIA 125

Query: 128 SDRPGENIFLFRKPLGVVAGILPWNFPFFLIARKMAPALLTGNTIVVKPSEETPNNCFEF 187
           SDR GE I+L R P+GVVAGILPWNFPF+LI RK+APAL+ GNTIV+KPSEETP N F F
Sbjct: 126 SDRKGETIYLNRVPIGVVAGILPWNFPFYLIGRKLAPALVAGNTIVIKPSEETPLNAFLF 185

Query: 188 ARLVAETDLPRGVFNVVCGAGQ-VGGALSSHPGVDLISFTGSVETGARIMAAAAPNLTKL 246
           A L  E  LP+GVFN+V G G+  G ALS HPG+DL+SFTGSV TG  IM AAA NLT++
Sbjct: 186 AELADEVGLPKGVFNMVSGRGRTTGAALSGHPGIDLVSFTGSVPTGVAIMEAAAKNLTRV 245

Query: 247 NLELGGKAPAIVLADADLELAVKAIRDSRIINSGQVCNCAERVYVQRQVAEPFIERIAAA 306
           NLELGGKAPAIVL DADL+LAV+AI  SR+IN+GQVCNCAER++V+RQVA+ F +R    
Sbjct: 246 NLELGGKAPAIVLKDADLDLAVEAITASRVINTGQVCNCAERIFVERQVADEFTDRFVKR 305

Query: 307 MAATRYGDPLAEPEVEMGPLINRLGLEKIDAKVRTALAQGATLVTGGAIAERP-GHHYQP 365
           MAA  YGDP+AEP V+MGPL+N L L+K++A V  A   GA++  GG  AER  GHHY+P
Sbjct: 306 MAAVTYGDPIAEPTVDMGPLVNALQLDKVEAMVERAREAGASVALGGKRAERNCGHHYEP 365

Query: 366 TVLTGCRADTRIMREEIFGPVLPIQIVDDLDEAIALANDCEYGLTSSVFTRDLNKAMHAL 425
           TVLTGC  D  IMR+EIFGPV PI +V+D DEA+  AND EYGLTSS++T+DLNKAM   
Sbjct: 366 TVLTGCTPDMEIMRKEIFGPVAPIAVVEDADEAVHYANDTEYGLTSSLYTQDLNKAMRVT 425

Query: 426 RELDFGETYINREHFEAMQGFHAGVRKSGIGGADGKHGLYEYTHTHVVYLQ 476
           R L FGETYINRE+ EA QGFHAG +KSGIGGADGKHG YEY  T  VY+Q
Sbjct: 426 RRLQFGETYINRENGEAYQGFHAGRKKSGIGGADGKHGFYEYMETQAVYIQ 476


Lambda     K      H
   0.320    0.136    0.395 

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: 652
Number of extensions: 26
Number of successful extensions: 3
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: 477
Length of database: 478
Length adjustment: 34
Effective length of query: 443
Effective length of database: 444
Effective search space:   196692
Effective search space used:   196692
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: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources