GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudomonas putida KT2440

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate PP_2049 PP_2049 Alcohol dehydrogenase, iron-containing

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__Putida:PP_2049
          Length = 387

 Score =  242 bits (617), Expect = 2e-68
 Identities = 149/372 (40%), Positives = 219/372 (58%), Gaps = 4/372 (1%)

Query: 17  GALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLET 76
           GA+ +L    +  GAK +L+I+DP + ++G++D +          V ++++V  +P    
Sbjct: 17  GAVQRLAGLCRERGAKRVLIISDPGIARLGMLDDLLPGFTAAKVGVAIFSEVTADPSEAC 76

Query: 77  GEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPK 136
              A   AR    DLV+G GGGS++D+AKL A+LA  D S      L G    + + LP 
Sbjct: 77  VLAAAQRARHIGADLVVGFGGGSSMDVAKLVALLAHRDCS-QPIAELYGIDRAKGRRLPL 135

Query: 137 ILIPTTSGTGSEVTNISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGID 195
           I +PTT+GTGSEVT I++++   TTK  +    LL D+A++D   T+ +P  VTAATGID
Sbjct: 136 IQVPTTAGTGSEVTPIAIVTTGATTKMGIVSPLLLPDLAVLDAVCTLGLPSAVTAATGID 195

Query: 196 ALTHAVEAYVS-VNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLA 254
           A+ HA+EAY S +  +P S  LA  A+RL++ +L +AV NG + QAR  M  G+ LAG A
Sbjct: 196 AMVHAIEAYTSRLKRNPLSSLLAREALRLLADNLDQAVHNGGNLQARQAMLLGACLAGQA 255

Query: 255 FFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADI-FNALGGNSS 313
           F NA VA VHALAYPLGG FH+ HG +NA++LP+V+ +         A++    LG    
Sbjct: 256 FANAPVAAVHALAYPLGGHFHVPHGLANALVLPHVLRFNLPVAAVDYAELAVPLLGARLQ 315

Query: 314 FLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLL 373
              + + + + V EL    +  G+P  L    +P   L  L +DA+QQ+RLL  +P  + 
Sbjct: 316 PGDQRQQAEQFVAELAALSSRCGLPDRLRDADVPRHRLGQLAEDAMQQQRLLVNNPREVT 375

Query: 374 EADIRAIYEAAF 385
           +AD  AIYEAA+
Sbjct: 376 QADALAIYEAAY 387


Lambda     K      H
   0.318    0.135    0.381 

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: 381
Number of extensions: 19
Number of successful extensions: 5
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: 395
Length of database: 387
Length adjustment: 31
Effective length of query: 364
Effective length of database: 356
Effective search space:   129584
Effective search space used:   129584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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