GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Herbaspirillum seropedicae SmR1

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase

Query= SwissProt::A1B4L2
         (508 letters)



>FitnessBrowser__HerbieS:HSERO_RS09465
          Length = 506

 Score =  814 bits (2103), Expect = 0.0
 Identities = 391/493 (79%), Positives = 438/493 (88%)

Query: 16  PFEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWG 75
           PF++RYDNFIGG++V PV G YF N +P+ G    ++ARS A D+ELALDAAHAAK+ WG
Sbjct: 14  PFKQRYDNFIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKKSWG 73

Query: 76  ATSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLR 135
            TSP ERAN++LKIADRME NLELLATAET DNGKPIRETMAAD+PLAIDHFRYFA  +R
Sbjct: 74  KTSPTERANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVR 133

Query: 136 AQEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQT 195
            QEGSI  ID+DT AYHFHEPLGVVGQIIPWNFP+LMA WKLAPA+AAGNCVVLKPAEQT
Sbjct: 134 TQEGSICPIDNDTYAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQT 193

Query: 196 PAGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYAS 255
           PA IMV   LI DL+PPGV+NIV GFG+EAGKPLAS+ RIAKIAFTGETTTGRLIMQYAS
Sbjct: 194 PASIMVLIELIADLIPPGVVNIVQGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYAS 253

Query: 256 ENLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESI 315
           +NLIPVTLELGGKSPNIFFADV  +DDDFFDKALEGF MFALNQGEVCTCPSRVL+QESI
Sbjct: 254 QNLIPVTLELGGKSPNIFFADVLDKDDDFFDKALEGFAMFALNQGEVCTCPSRVLVQESI 313

Query: 316 YDKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAA 375
           Y++F+ERA++RV AIKQG+P +  TMIGAQAS EQ EKILSY+DIGK+EGA+VL GG   
Sbjct: 314 YERFIERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGGGRE 373

Query: 376 DLGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAG 435
           +LGG+L+ GYY++PT+F+GNNKMRIFQEEIFGPVVSVTTFKD+ EAL IANDTLYGLGAG
Sbjct: 374 ELGGDLASGYYVKPTVFQGNNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGLGAG 433

Query: 436 VWSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKN 495
           +W+RD    +RMGR I+AGRVWTNCYH YPAHAAFGGYKQSGIGRE HKMMLDHYQQTKN
Sbjct: 434 LWTRDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKN 493

Query: 496 MLVSYSPKKLGFF 508
           +LVSYSPK LGFF
Sbjct: 494 LLVSYSPKALGFF 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: 892
Number of extensions: 24
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.

Links

Downloads

Related tools

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