Aligments for a candidate for iolA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for iolA in Klebsiella michiganensis M5al

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BWI76_RS03070 BWI76_RS03070 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS03070 BWI76_RS03070
           methylmalonate-semialdehyde dehydrogenase (CoA
           acylating)
          Length = 501

 Score =  558 bits (1439), Expect = e-163
 Identities = 274/497 (55%), Positives = 363/497 (73%), Gaps = 4/497 (0%)

Query: 6   VVGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSS 65
           + G++I G+   S + +   VF+PATG V   V L+    V  A+  A  AF +WS  + 
Sbjct: 3   ITGNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRTTP 62

Query: 66  LRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTD 125
           LRR+RVMF FK LL++H +ELA II  EHGKV SDA GE+TRG+E+VE+ACG P+L+K +
Sbjct: 63  LRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIKGE 122

Query: 126 FSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSAS 185
           FS ++G G+D+++L QPLGV AG+TPFNFP MVP+WM PLAL  GN F+LKP    P+A+
Sbjct: 123 FSSDVGTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSFVLKPPALAPTAA 182

Query: 186 LLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGK 245
           + +A LL EAGLPDGVFNVV       + L + P I A+SFVGS+ +AE+I++  +A GK
Sbjct: 183 VRLAELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRIAAVSFVGSSGVAEHIYKTASAYGK 242

Query: 246 RVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGD-VGDELIAKL 304
           RVQA G AKNH IVMPDADLD   +A++G A+GSAGERCMA+ + VAVGD   D+LIA+L
Sbjct: 243 RVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIARL 302

Query: 305 LPRIDQLKIGNGQQPG---TDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGA 361
            P ++ LK+G G   G    +MGP+V+  H+ KV G+ID GV+EGA L+VDGR  +VPG 
Sbjct: 303 KPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVPGF 362

Query: 362 EQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRD 421
           E+G++VG TLFD VT EM+I+++EIFGPVLGIVRV D+ +A+ L+N+HEFGNG + FT +
Sbjct: 363 EEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFTSN 422

Query: 422 GGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVM 481
           G  AR F   ++ GMVG+NVP+PVPMA+HSFGGWKRS+FG  + +G +G+RFY+R K+  
Sbjct: 423 GHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKTAT 482

Query: 482 QRWPDSIAKGPEFSMPT 498
            RWP       EFSMPT
Sbjct: 483 VRWPQGQQTVSEFSMPT 499


Lambda     K      H
   0.320    0.137    0.412 

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: 719
Number of extensions: 23
Number of successful extensions: 3
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: 500
Length of database: 501
Length adjustment: 34
Effective length of query: 466
Effective length of database: 467
Effective search space:   217622
Effective search space used:   217622
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 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, or view the source code.

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