Alignments for a candidate for ARO10 in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for ARO10 in Klebsiella michiganensis M5al

Align pyruvate decarboxylase (EC 4.1.1.1) (characterized)
to candidate BWI76_RS20520 BWI76_RS20520 indolepyruvate decarboxylase

Query= BRENDA::P16467
         (563 letters)



>FitnessBrowser__Koxy:BWI76_RS20520
          Length = 553

 Score =  360 bits (925), Expect = e-104
 Identities = 217/563 (38%), Positives = 308/563 (54%), Gaps = 21/563 (3%)

Query: 5   TLGKYLFERLSQVNCNTVFGLPGDFNLSLLDKLYEVKGMRWAGNANELNAAYAADGYARI 64
           T+G YL +RL     + +FG+PGD+NL  LD +   + + W G ANELNAAYAADGYARI
Sbjct: 6   TIGDYLLDRLVDCGIDRLFGVPGDYNLQFLDSVIAHRNLGWVGCANELNAAYAADGYARI 65

Query: 65  KGMSCIITTFGVGELSALNGIAGSYAEHVGVLHVVGVPSISSQAKQLLLHHTLGNGDFTV 124
           KG   ++TT+GVGELSALNGIAGSYAEHV VLH+VG P   +Q +  LLHHTLG+GDF+ 
Sbjct: 66  KGAGALLTTYGVGELSALNGIAGSYAEHVPVLHIVGAPCTGAQQRGELLHHTLGDGDFSH 125

Query: 125 FHRMSANISETTAMITDIANAPAEIDRCIRTTYTTQRPVYLGLPANLVDLNVPAKLLETP 184
           F RMS  I+ + A++    NA  EIDR +    T  RP YL LPA++      AK   TP
Sbjct: 126 FSRMSEQITCSQAVLA-AGNACHEIDRVLSEMLTHHRPGYLMLPADV------AKAKTTP 178

Query: 185 ----IDLSLKPNDAEAEAEVVRTVVELIKDAKNPVILADACASRHDVKAETKKLMDLTQF 240
               + +   P D    A        +++ ++   +LAD  A R+ ++   ++ +     
Sbjct: 179 PAHRLLIQGLPADENQLAGFREHAGRMLRSSRRVSLLADFLAQRYGLQNALREWVAKVPV 238

Query: 241 PVYVTPMGKGAIDEQHPRYGGVYVGTLSRPEVKKAVESADLILSIGALLSDFNTGSFSYS 300
                 MGKG  DEQ   + G Y G  S  E + A+E+AD I+ IG   +D  T  F+  
Sbjct: 239 AYATMLMGKGLFDEQQSGFVGTYSGIASAEETRDAIENADTIICIGTRFTDTITAGFTQH 298

Query: 301 YKTKNIVEFHSDHIKIRNATFPGVQMKFALQKLLDAIPEVVKDYKPVAVPARVPITKSTP 360
              +  +E     +++ +  F  + M+ AL  L++    +  ++  V+   + P     P
Sbjct: 299 LPLEKTIEIQPFAVRVADRWFSRIPMEKALAILIELSASLAAEW--VSPNIQAPGVSGAP 356

Query: 361 ANTPMKQEWMWNHLGNFLREGDIVIAETGTSAFGINQTTFPTDVYAIVQVLWGSIGFTVG 420
             + + Q+  WN +   LR GDI++A+ GT+AFG      P D   IVQ LWGSIGFT+ 
Sbjct: 357 EGS-LTQKNFWNTVQKQLRPGDIILADQGTAAFGAAALKLPVDATLIVQPLWGSIGFTLP 415

Query: 421 ALLGATMAAEELDPKKRVILFIGDGSLQLTVQEISTMIRWGLKPYIFVLNNNGYTIEKLI 480
           A  GA +AA E    +RV+L +GDG+ QLT+QE+ +M+R   +P I +LNN GYT+E+ I
Sbjct: 416 AAYGAQIAAAE----RRVVLIVGDGAAQLTIQELGSMLRDKQRPLILLLNNEGYTVERAI 471

Query: 481 HGPHAEYNEIQGWDHLALLPTFGAR-NYETHRVATTGEWEKLTQDKDFQDNSKIRMIEVM 539
           HGP   YN+I  WD   L   F         RV  T E ++        D  ++ ++EVM
Sbjct: 472 HGPEQRYNDIALWDWNRLPDAFAPDVPSRCWRVTRTQELQEAMNSSVASD--RLTLVEVM 529

Query: 540 LPVFDAPQNLVKQAQLTAATNAK 562
           LP  D P  L    Q     N++
Sbjct: 530 LPKMDIPDFLRTVTQALEERNSR 552


Lambda     K      H
   0.318    0.134    0.395 

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: 763
Number of extensions: 29
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: 563
Length of database: 553
Length adjustment: 36
Effective length of query: 527
Effective length of database: 517
Effective search space:   272459
Effective search space used:   272459
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources