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 LdcA; EC 4.1.1.18 (characterized)
to candidate BWI76_RS24175 BWI76_RS24175 ornithine decarboxylase

Query= SwissProt::Q9I2S7
         (751 letters)



>FitnessBrowser__Koxy:BWI76_RS24175
          Length = 712

 Score =  354 bits (909), Expect = e-102
 Identities = 222/618 (35%), Positives = 316/618 (51%), Gaps = 14/618 (2%)

Query: 135 QVARAARNYLAGLLPPFFRALVEHTAQSNYSWHTPGHGGGVAYRKSPVGQAFHQFFGENT 194
           ++  AA  Y   LLPPFF  L ++    N ++  PGH  G  ++K P G+ F  FFGEN 
Sbjct: 87  ELEAAACGYEENLLPPFFDTLTQYVEMDNSTFACPGHQHGAFFKKHPAGRQFFDFFGENV 146

Query: 195 LRSDLSVSVPELGSLLDHTGPLAEAEDRAARNFGADHTFFVINGTSTANKIVWHSMVGRE 254
            R+D+  +  +LG LL H G    A+  AA+ F AD T+FV+NGTS ANK+V ++++ R 
Sbjct: 147 FRADMCNADVKLGDLLIHEGSAKHAQKFAAKVFNADKTYFVLNGTSAANKVVTNALLTRG 206

Query: 255 DLVLVDRNCHKSILH-SIIMTGAIPLYLTPERNELGIIGPIPLSEFSKQSIAAKIAASPL 313
           DLVL DRN HKS  H ++I  GA P+YL   RN  G IG I    F ++ +   I  +  
Sbjct: 207 DLVLFDRNNHKSNHHGALIQAGATPVYLEASRNPFGFIGGIDDRCFDEKYLRDLIRETAP 266

Query: 314 ARGREPK-VKLAVVTNSTYDGLCYNAELIKQTLGDSVEVLHFDEAWYAYAAFHEFYDGRY 372
            +   P+  +LAV+   TYDG  YNA  +   +G   + + FD AW  Y  F        
Sbjct: 267 EKADMPRPFRLAVIQLGTYDGTVYNARQVVDKIGSLCDYILFDSAWVGYEQFIPMMADCS 326

Query: 373 GMGTSRSEEGPLVFATHSTHKMLAAFSQASMIHVQD----GGTRKLDVARFNEAFMMHIS 428
            +    + + P +F T S HK  A FSQ S IH +D    G  R     R N AFM+H S
Sbjct: 327 PLLLDLTPDDPGIFVTQSVHKQQAGFSQTSQIHKKDNHLRGQERFCPHKRLNNAFMLHAS 386

Query: 429 TSPQYGIIASLDVASAMMEGPAGRSLIQETFDEALSFRRALANVRQNLDRNDWWFGVWQP 488
           TSP Y + A+LDV + + EG +GR L  E     +  R+A+    + +          +P
Sbjct: 387 TSPFYPLFAALDVNAKIHEGESGRRLWAECVALGIEARKAIIANCKMIQPFIPPVVAGRP 446

Query: 489 EQVEGTDQVGTHD--WVLEPSADWHGFGDIAEDYVLLDPIKVTLTTPGLSA-GGKLSEQG 545
            Q   T+ +      +  EP A WHGF   A D   +DP K+ LTTPG+ A  GK ++ G
Sbjct: 447 WQDHPTEAIARERRFFSFEPGARWHGFEGYASDQYFVDPCKLLLTTPGIDAESGKYTDFG 506

Query: 546 IPAAIVSRFLWERGLVVEKTGLYSFLVLFSMGITKGKWSTLVTELLEFKRCYDANLPLLD 605
           IPA I++ +L E G+V EK  L S L L +   +  K + LV  L  F++  +++ PL D
Sbjct: 507 IPATILAHYLRENGIVPEKCDLNSILFLLTPAESAEKLAQLVAMLARFEQHIESDTPLAD 566

Query: 606 VLPSVAQAGGKRYNGVGLRDLSDAMHASYRDNATAKAMKRMY--TVLPEVAMRPSEAYDK 663
           VLP++      RY    +R+L   MH  Y         K M+     P   M P +A  +
Sbjct: 567 VLPTIFNKYPVRYRDYTIRELCQEMHNLYVSFDVKDLQKEMFRKKSFPRAVMNPQDANRE 626

Query: 664 LVRGEVEAVPIARLEGRIAAVMLVPYPPGIPLIMPGERFTEATRSILDYLEFARTFERAF 723
            +RG VE V ++  EGRIAA   +PYPPG+  ++PGE +  A   +L Y           
Sbjct: 627 FIRGNVELVRLSAAEGRIAAEGALPYPPGVLCVVPGEIWGGA---VLRYFLALEEGVNML 683

Query: 724 PGFDSDVHGLQHQDGPSG 741
           PGF  ++ G+  +  P G
Sbjct: 684 PGFSPELQGVYSETDPDG 701


Lambda     K      H
   0.320    0.136    0.407 

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: 1191
Number of extensions: 67
Number of successful extensions: 8
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: 751
Length of database: 712
Length adjustment: 40
Effective length of query: 711
Effective length of database: 672
Effective search space:   477792
Effective search space used:   477792
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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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