GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Kocuria flava HO-9041

Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate WP_083529425.1 AS188_RS11615 aldehyde dehydrogenase family protein

Query= BRENDA::P51648
         (485 letters)



>NCBI__GCF_001482365.1:WP_083529425.1
          Length = 506

 Score =  363 bits (933), Expect = e-105
 Identities = 193/445 (43%), Positives = 273/445 (61%), Gaps = 8/445 (1%)

Query: 1   MELEVRRVRQAFLSGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLCKSEFNVYSQE 60
           ++  V R R AF+      L  RL +L+ L  +V+E  +++  A+AADL K     +  E
Sbjct: 46  VDAAVARARAAFVPDLG--LEARLDRLDRLETLVREHREELEEALAADLGKPRQEAWLTE 103

Query: 61  VITVLGEIDFMLENLPEWVTAKPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQ 120
           +   L E+  +   LP W   +  +  +      A  + Q LG VL+I  WNYP  L + 
Sbjct: 104 LAFTLEEVAGLRRGLPRWTAPERTRVPLSLAPARARTERQALGTVLVIAPWNYPVQLVLG 163

Query: 121 PLIGAIAAGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDH 180
           PL GA+AAGN V++KPSE++ + A++LA+LL Q+L  D   V+ GGV ETT LL+ RFDH
Sbjct: 164 PLAGALAAGNTVVVKPSEVTPSVARVLARLLEQHLG-DCTSVVEGGVPETTRLLEHRFDH 222

Query: 181 IFYTGNTAVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQT 240
           +FYTGN  V ++V  AAA+HLTPVTLELGGKSP ++D   DL    RRI WGKY+N GQT
Sbjct: 223 VFYTGNARVARVVAAAAARHLTPVTLELGGKSPAWVDATTDLRTAARRIVWGKYLNAGQT 282

Query: 241 CIAPDYILCEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLL---EG 297
           C+APD++L        +  ++   V++F+GE+ + S  Y RI+  RH +R+  LL     
Sbjct: 283 CVAPDHVLGTPEALAALEPELVRAVRQFHGEDPRRSGSYGRIVTERHLERLTRLLGQVPA 342

Query: 298 QKIAFGGETDEATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREK 357
           + +  GG+ + A RY+APTV+    P    M EEIFGP+LP+VPV + + A+  I   EK
Sbjct: 343 EDVVCGGQAEPAERYLAPTVVRSA-PDGPFMAEEIFGPVLPLVPVDSAEAAVGLITAGEK 401

Query: 358 PLALYVFSHNHKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFD 417
           PLALYVFS +  + +     TSSGG++ N  ++H +    PFGGVG+SG GAYHG+HSF+
Sbjct: 402 PLALYVFSEDPAVRELFARRTSSGGLSYNAPLLHLSHPGLPFGGVGASGTGAYHGRHSFE 461

Query: 418 TFSHQRPCLLKSLKREGANKLRYPP 442
           TFSH+R  L K  +     ++ YPP
Sbjct: 462 TFSHRRAVLDKP-QAPDTLRVVYPP 485


Lambda     K      H
   0.321    0.139    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: 533
Number of extensions: 21
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: 485
Length of database: 506
Length adjustment: 34
Effective length of query: 451
Effective length of database: 472
Effective search space:   212872
Effective search space used:   212872
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 (21.9 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