Alignments for a candidate for adh in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Caulobacter crescentus NA1000

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase

Query= SwissProt::A1B4L2
         (508 letters)



>FitnessBrowser__Caulo:CCNA_03695
          Length = 506

 Score =  830 bits (2145), Expect = 0.0
 Identities = 398/493 (80%), Positives = 442/493 (89%)

Query: 16  PFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWG 75
           PF+ RYDNFIGG+WVAP  GRYF N++PI G +I +IARS+A DIE ALDAAHAAK  W 
Sbjct: 14  PFKARYDNFIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAAKAGWA 73

Query: 76  ATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLR 135
            TS A+R+ I+L+IADRME NL  LATAETWDNGKPIRET+AAD+PLAIDHFRYFAG LR
Sbjct: 74  RTSAADRSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGCLR 133

Query: 136 AQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQT 195
           +QEGSIS+ID DT+AYHFHEPLGVVGQIIPWNFPLLMACWKLAPA+AAGNCVVLKPAEQT
Sbjct: 134 SQEGSISEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQT 193

Query: 196 PAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYAS 255
           PA IMVWA +IGDLLP GVLNIVNGFGLEAGKPLASS RIAKIAFTGET+TGRLIMQYA+
Sbjct: 194 PASIMVWAEMIGDLLPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYAA 253

Query: 256 ENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESI 315
           +NLIPVTLELGGKSPNIFF DVAREDDD+ DKALEGFTMFALNQGEVCTCPSR L+QESI
Sbjct: 254 QNLIPVTLELGGKSPNIFFDDVAREDDDYLDKALEGFTMFALNQGEVCTCPSRALVQESI 313

Query: 316 YDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAA 375
           Y+KFMERA++RV A+ QG P +  TMIGAQAS EQ  KIL Y+DIG+ EGA++L GG+  
Sbjct: 314 YEKFMERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRK 373

Query: 376 DLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAG 435
            L G+L+ GYY+EPT+F G+NKMRIFQEEIFGPV++VTTFK + EALEIANDT +GLGAG
Sbjct: 374 ILPGQLADGYYVEPTVFEGHNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGAG 433

Query: 436 VWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 495
           VWSRDAN CYR GRGI+AGRVWTNCYHAYPAHAAFGGYKQSG+GRETHKMMLDHYQQTKN
Sbjct: 434 VWSRDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTKN 493

Query: 496 MLVSYSPKKLGFF 508
           MLVSYSPK LGFF
Sbjct: 494 MLVSYSPKALGFF 506


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: 897
Number of extensions: 27
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: 506
Length adjustment: 34
Effective length of query: 474
Effective length of database: 472
Effective search space:   223728
Effective search space used:   223728
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 (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 paper from 2022 on GapMind for carbon sources, 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

GapMind for catabolism of small carbon sources