Alignments for a candidate for cadA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for cadA in Klebsiella michiganensis M5al

Align lysine decarboxylase (EC 4.1.1.18) (characterized)
to candidate BWI76_RS05300 BWI76_RS05300 lysine decarboxylase LdcC

Query= BRENDA::A0A0H3FP92
         (712 letters)



>FitnessBrowser__Koxy:BWI76_RS05300
          Length = 712

 Score = 1400 bits (3624), Expect = 0.0
 Identities = 681/712 (95%), Positives = 695/712 (97%)

Query: 1   MNIIAIMGPHGVYHKDEPIKELEAALQKQGFQTIWPQNSADLLQFIEHNPRICGVIFDWD 60
           MNIIAIMGPHGVY+KDEPIKELEAALQ+QGFQTIWPQNSADLLQFIEHNPRICGVIFDWD
Sbjct: 1   MNIIAIMGPHGVYYKDEPIKELEAALQRQGFQTIWPQNSADLLQFIEHNPRICGVIFDWD 60

Query: 61  EYSVDLCSDINRLNEYLPLYAFINTHSTMDVSSQDLRMALWFFEYALGLAEDIATRIRQY 120
           EYSVDLCSDINRLNEYLPLYAFIN HSTMDVSSQDLRM LWFFEYALGLAE+IATRI QY
Sbjct: 61  EYSVDLCSDINRLNEYLPLYAFINAHSTMDVSSQDLRMTLWFFEYALGLAEEIATRIGQY 120

Query: 121 TNEYLDNITPPFTKALFNYVQEGKYTFCTPGHMAGTAYQKSPVGCLFYDFFGGNTLKADV 180
           T EYLDNITPPFTKALFNYVQEGKYTFCTPGHM G+AYQKSPVGCLFYDFFGGNTLKADV
Sbjct: 121 TREYLDNITPPFTKALFNYVQEGKYTFCTPGHMGGSAYQKSPVGCLFYDFFGGNTLKADV 180

Query: 181 SISVTELGSLLDHTGPHLEAEEYIARAFGAEQSYMVTNGTSTSNKIVGMYSAPAGSTLLI 240
           SISVTELGSLLDH+GPHLEAEEYIARAFGAEQSYMVTNGTSTSNKIVGMYSAPAGSTLLI
Sbjct: 181 SISVTELGSLLDHSGPHLEAEEYIARAFGAEQSYMVTNGTSTSNKIVGMYSAPAGSTLLI 240

Query: 241 DRNCHKSLAHLLMMSDIVPLWLKPTRNALGILGGIPKREFTRDSVQHKVETTRGAQWPVH 300
           DRNCHKSLAHLLMMSD+VPLWLKPTRNALGILGGIPKREFTRDS+Q KV TT GA WPVH
Sbjct: 241 DRNCHKSLAHLLMMSDVVPLWLKPTRNALGILGGIPKREFTRDSIQQKVNTTGGAGWPVH 300

Query: 301 AVITNSTYDGLLYNTTWIKQTLDVPSIHFDSAWVPYTHFHPIYQGKSGMSGDRVPGKVIF 360
           AVITNSTYDGLLYNTTWIK+TLDVPSIHFDSAWVPYTHFHPIYQGKSGMSGDR+PGKVIF
Sbjct: 301 AVITNSTYDGLLYNTTWIKETLDVPSIHFDSAWVPYTHFHPIYQGKSGMSGDRIPGKVIF 360

Query: 361 ETQSTHKMLAALSQASLIHIKGSYDEDTFNEAFMMHTSTSPSYPIVASIETAAAMLRGNS 420
           ETQSTHKMLAALSQASLIHIKGSYDEDTFNEAFMMHTSTSPSYPIVASIETAAAMLRGNS
Sbjct: 361 ETQSTHKMLAALSQASLIHIKGSYDEDTFNEAFMMHTSTSPSYPIVASIETAAAMLRGNS 420

Query: 421 GKRLIQRSIERALHFRKEVQRLREEADGWFFDIWQPEEVDEAQCWPVSPGEAWHGFQDAD 480
           G+RLIQRSIERAL FRKEVQRLREE+DGWFFDIWQPEEV EAQCWPVSPGE WHGFQDAD
Sbjct: 421 GRRLIQRSIERALDFRKEVQRLREESDGWFFDIWQPEEVGEAQCWPVSPGEQWHGFQDAD 480

Query: 481 DDHMFLDPVKVTILTPGMDEQGNMAEEGIPAALVAKFLDERGVVVEKTGPYNLLFLFSIG 540
           DDHMFLDPVKVTILTPGMDEQGNM  EGIPAALVAKFLDERGVVVEKTGPYNLLFLFSIG
Sbjct: 481 DDHMFLDPVKVTILTPGMDEQGNMDSEGIPAALVAKFLDERGVVVEKTGPYNLLFLFSIG 540

Query: 541 IDKTRAMGLLRGLTEFKRAYDLNLRVKNMLPDLYAEDPDFYRNMRIQDLAQGIHRLIRQH 600
           IDKTRAMGLLRGLTEFKR+YDLNLRVKNMLPDLYAEDPDFYRNMRIQDLAQGIHRLIRQH
Sbjct: 541 IDKTRAMGLLRGLTEFKRSYDLNLRVKNMLPDLYAEDPDFYRNMRIQDLAQGIHRLIRQH 600

Query: 601 QLSQLMLRAFDVLPEMKMTPHQAWQRQIKGEVETIELENLVGRISANMILPYPPGVPLLM 660
           QLSQLML AFDVLPEMKMTPHQAWQRQIKGEVETIELENLVGRISANMILPYPPGVPLLM
Sbjct: 601 QLSQLMLSAFDVLPEMKMTPHQAWQRQIKGEVETIELENLVGRISANMILPYPPGVPLLM 660

Query: 661 PGEMITEESRAVLDFLLMLCSIGRHYPGFETDIHGAKRDEDGVYRVRVLKNN 712
           PGEMI EESRAVL+FLLMLCSIGRHYPGFETDIHGAKRDEDGVY VRVLKN+
Sbjct: 661 PGEMIVEESRAVLNFLLMLCSIGRHYPGFETDIHGAKRDEDGVYWVRVLKND 712


Lambda     K      H
   0.321    0.137    0.419 

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: 1761
Number of extensions: 36
Number of successful extensions: 1
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: 712
Length of database: 712
Length adjustment: 39
Effective length of query: 673
Effective length of database: 673
Effective search space:   452929
Effective search space used:   452929
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: 55 (25.8 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