GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Brucella inopinata BO1

Align 4-trimethylaminobutyraldehyde dehydrogenase; TMABA-DH; TMABADH; Aldehyde dehydrogenase family 9 member A1; EC 1.2.1.47; EC 1.2.1.3 (characterized)
to candidate WP_008508467.1 BIBO1_RS14100 betaine-aldehyde dehydrogenase

Query= SwissProt::Q19A30
         (505 letters)



>NCBI__GCF_000182725.1:WP_008508467.1
          Length = 487

 Score =  485 bits (1248), Expect = e-141
 Identities = 242/467 (51%), Positives = 326/467 (69%), Gaps = 10/467 (2%)

Query: 41  PVFEPATGRVLCQMVPCGAEEVDEAIMSAHAAYVQWSKKSGTERARVMLEAARIIRERRE 100
           PV  PAT   +  +       ++ A  +A  A  +W+     ER R++   A I+RE+  
Sbjct: 25  PVIYPATSEEIASLYSATPGIIEAAYAAALKAQGEWAALKPVERGRILRRTAEILREKNR 84

Query: 101 KIAKLEVINNGKSITEALV-DIDVAWQCIEYYAGVAGTLAGQHFQLPGGAFAYTRREPLG 159
           K++KLE ++ GK++ E LV D   A   +E++ G+     G+  +L GG+FAYTRRE LG
Sbjct: 85  KLSKLETLDTGKALQETLVADAASAADALEFFGGIISGFNGEFVEL-GGSFAYTRREALG 143

Query: 160 VCVGIGAWNYPFQIAACKSAPALACGNAMVFKPSPFTPVTAVILAEIYKEAGVPDGLFCV 219
           +CVGIGAWNYP QIAA KSAPALA GNA +FKPS  TP++A+ LAE YKEAG+PDGLF V
Sbjct: 144 ICVGIGAWNYPIQIAAWKSAPALAMGNAFIFKPSENTPLSALALAEAYKEAGLPDGLFNV 203

Query: 220 VQGGAETGSLLCNHPKVAKVSFTGSVPTGKKVMEMSAKGVKQVTLELGGKSPLIIFKDCD 279
           VQG  + G+ L NH   AKVS TGSVPTG+++M  + + +K VT+ELGGKSPLI+F D D
Sbjct: 204 VQGYGDVGAALVNHRLTAKVSLTGSVPTGRRIMAQAGEQLKHVTMELGGKSPLIVFDDAD 263

Query: 280 LENAVKGALMANFLTQGQVCCNGTRVFVHKDILPQFLEEVVKRTKAIAVGDPLLDSTRMG 339
           LE+A+ GA++ NF + GQVC NGTRVFVHK+I  +F+E +V+RT+ I +GDP  ++T+MG
Sbjct: 264 LESAIGGAMLGNFYSTGQVCSNGTRVFVHKNIRERFIERLVERTRKIRIGDPFDEATQMG 323

Query: 340 ALITKPHLEKVLGFVRQAKKEGGRVLCGGEPFVPSDPKLKG---GYFMSPCILDNCRDDM 396
            LI+    +KVL ++++ K EG  + CGG       PKL+G   G+F+ P +  +  D M
Sbjct: 324 PLISAAQRDKVLSYIKKGKAEGATLACGG-----GVPKLQGFDKGFFIEPTVFTDVTDTM 378

Query: 397 TCVKEEIFGPVMSVLPFDTEEEVIRRANNTTFGLASGVFTRDISRAHRVAASLEAGTCFI 456
           T  +EEIFGP+MSVL F  E+EVI RAN++ FGLA+GVFT D+SR HRV   ++AGTC+I
Sbjct: 379 TIAREEIFGPLMSVLEFSDEDEVIARANDSEFGLAAGVFTADLSRGHRVIGQIKAGTCWI 438

Query: 457 NNYNISPVEVPFGGYKMSGFGRENGQVTIEYYSQLKTVVVETGDVEN 503
           N YN++PVEVPFGGYK SG GRENG   + +YSQ+KTV VE G V++
Sbjct: 439 NAYNLTPVEVPFGGYKQSGIGRENGIAALAHYSQIKTVYVEMGKVDS 485


Lambda     K      H
   0.320    0.136    0.410 

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: 678
Number of extensions: 16
Number of successful extensions: 4
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: 505
Length of database: 487
Length adjustment: 34
Effective length of query: 471
Effective length of database: 453
Effective search space:   213363
Effective search space used:   213363
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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