GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Pedobacter sp. GW460-11-11-14-LB5

Align Aldehyde dehydrogenase; Acetaldehyde dehydrogenase; EC 1.2.1.3 (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= SwissProt::A1B4L2
         (508 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  686 bits (1771), Expect = 0.0
 Identities = 330/492 (67%), Positives = 397/492 (80%)

Query: 17  FEERYDNFIGGEWVAPVSGRYFTNTTPITGAEIGQIARSEAGDIELALDAAHAAKEKWGA 76
           F+ +YDN+IGG++VAPV G YF N +PI G    + A S   D+ELA+DAAH A + W  
Sbjct: 10  FKPQYDNYIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSK 69

Query: 77  TSPAERANIMLKIADRMERNLELLATAETWDNGKPIRETMAADLPLAIDHFRYFAGVLRA 136
           TS  ER+ I+ KIA RME NLE LA  ET DNGK +RET+AADLPL +DHFRYFAGV+RA
Sbjct: 70  TSSTERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRA 129

Query: 137 QEGSISQIDDDTVAYHFHEPLGVVGQIIPWNFPLLMACWKLAPAIAAGNCVVLKPAEQTP 196
           +EGS+S++D +TV+   HEP+GVV QIIPWNFPLLM  WKLAPA+AAGNCVVLKPAE TP
Sbjct: 130 EEGSLSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTP 189

Query: 197 AGIMVWANLIGDLLPPGVLNIVNGFGLEAGKPLASSNRIAKIAFTGETTTGRLIMQYASE 256
             IMV   LIGDLLPPGV+N+VNGFG E G+ L ++ +++K AFTG T TGRL+MQYA+E
Sbjct: 190 VSIMVLMELIGDLLPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATE 249

Query: 257 NLIPVTLELGGKSPNIFFADVAREDDDFFDKALEGFTMFALNQGEVCTCPSRVLIQESIY 316
           N+IPVTLELGGKSPNIFF+ V  EDD F DKA+EG  MFALNQGE+CTCPSR+LIQE IY
Sbjct: 250 NIIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFALNQGEICTCPSRLLIQEDIY 309

Query: 317 DKFMERAVQRVQAIKQGDPRESDTMIGAQASSEQKEKILSYLDIGKKEGAEVLTGGKAAD 376
           +KF+ + ++R +AIK G P +   M+GAQAS  Q EKI +Y+ +GK+EGAEVLTGG+  +
Sbjct: 310 EKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINE 369

Query: 377 LGGELSGGYYIEPTIFRGNNKMRIFQEEIFGPVVSVTTFKDQAEALEIANDTLYGLGAGV 436
           L GEL GGYYI+PTIF+G+NKMRIFQEEIFGPV++VTTFK   EA+EIANDTLYGLGAGV
Sbjct: 370 LPGELGGGYYIKPTIFKGHNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGV 429

Query: 437 WSRDANTCYRMGRGIKAGRVWTNCYHAYPAHAAFGGYKQSGIGRETHKMMLDHYQQTKNM 496
           W+RDA+  Y++ R I+AGRVW N YHAYPA A FGGYKQSG+GRE HKMML HY+QTKNM
Sbjct: 430 WTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKNM 489

Query: 497 LVSYSPKKLGFF 508
           L+SY   KLGFF
Sbjct: 490 LISYDKNKLGFF 501


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: 809
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: 501
Length adjustment: 34
Effective length of query: 474
Effective length of database: 467
Effective search space:   221358
Effective search space used:   221358
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:

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