GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF in Klebsiella michiganensis M5al

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase

Query= BRENDA::Q97UA1
         (478 letters)



>FitnessBrowser__Koxy:BWI76_RS12820
          Length = 499

 Score =  279 bits (714), Expect = 1e-79
 Identities = 173/444 (38%), Positives = 255/444 (57%), Gaps = 16/444 (3%)

Query: 41  DVKEAINKAVAKF--DEWS-RTPAPKRGSILLKAGELMEQEAQEFALLMTLEEGKTLKDS 97
           DV  A+  A   F    W+ RTPA  R  ILL+  +L+EQ  +E A L TLE+GK++  S
Sbjct: 58  DVDRAVMSAWRAFVSRSWAGRTPAD-RERILLRFADLVEQHGEELAQLETLEQGKSINIS 116

Query: 98  M-FEVTRSYNLLKFYGALAFKISGKTLPSADP-----NTRIFTVKEPLGVVALITPWNFP 151
             FEV  + N +++   L  KISG+TL  + P       + +T KEP+GVVA I PWNFP
Sbjct: 117 RAFEVGCTLNWMRYTAGLTTKISGRTLDVSIPFPAGGRYQAWTKKEPVGVVAGIVPWNFP 176

Query: 152 LSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGLPEGVVNLVVGKGSEVGDT 211
           L I +WK+ PALAAG + VIKP+  TPL + ++ E+ ++AG+P+GV N+V G G+  G  
Sbjct: 177 LMIGMWKVMPALAAGCSIVIKPSETTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGAA 236

Query: 212 IVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSADLTLAAELA 271
           + S   +A VSFTGST  GK+I ++    +R+TR+ LELGGKN   V K AD     E  
Sbjct: 237 LTSHPLVAKVSFTGSTATGKQIARVAA--DRLTRVTLELGGKNPAIVLKDADPQWVIEGL 294

Query: 272 VRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVGPG-TEDVDMGPVVDEGQF 330
           + G F   GQ C A+SR+ I   ++        + VK  +VGPG  E   + PVV +   
Sbjct: 295 MTGSFLNQGQVCAASSRIYIEAPLFDTLVSGFEQAVKSLQVGPGMLESSQINPVVSQAHC 354

Query: 331 KKDLEYIEYGKNVGAKLIYGGNIIPGKGYFLEPTIFEGVTSDMRLFKEEIFGPVLSVTEA 390
            K   Y++  +   A+LI G      +GY++ PT+     + +RL +EE+FGPV+++   
Sbjct: 355 AKVAAYLDEARQQKAELISGHAGPDAQGYYIAPTLVINPDAGLRLCREEVFGPVVNLVRV 414

Query: 391 KDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVEAGVIKVNKPTVGLELQAPFGGFK 450
            D +EA+ L N  D+G TA +   D+     +  R++AG + VN  T+ ++   PFGG K
Sbjct: 415 ADGEEALLLANDSDFGLTASVWTRDLTQALSYTDRLQAGTVWVNSHTL-IDANLPFGGMK 473

Query: 451 NSGATTWKEMGEDALEFYLKEKTV 474
            SG  T ++ G D L+ + + K+V
Sbjct: 474 QSG--TGRDFGPDWLDDWCETKSV 495


Lambda     K      H
   0.316    0.135    0.389 

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: 608
Number of extensions: 33
Number of successful extensions: 6
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: 478
Length of database: 499
Length adjustment: 34
Effective length of query: 444
Effective length of database: 465
Effective search space:   206460
Effective search space used:   206460
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 (21.6 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