Aligments for a candidate for adiA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for adiA in Klebsiella michiganensis M5al

Align arginine decarboxylase (EC 4.1.1.19) (characterized)
to candidate BWI76_RS05300 BWI76_RS05300 lysine decarboxylase LdcC

Query= BRENDA::P28629
         (755 letters)



>FitnessBrowser__Koxy:BWI76_RS05300
          Length = 712

 Score =  461 bits (1185), Expect = e-134
 Identities = 261/735 (35%), Positives = 403/735 (54%), Gaps = 44/735 (5%)

Query: 21  VERLADALSQQNVTVIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLH 80
           ++ L  AL +Q    I   +  D    +  N  I  ++F +     D   ++ +L     
Sbjct: 19  IKELEAALQRQGFQTIWPQNSADLLQFIEHNPRICGVIFDWDEYSVDLCSDINRL----- 73

Query: 81  ERQQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIAGRAVAAMTRYRQQLLP 140
              + +P++   +    +    +DL   +  F + L   A+ IA R       Y   + P
Sbjct: 74  --NEYLPLYAFINAHSTMDVSSQDLRMTLWFFEYAL-GLAEEIATRIGQYTREYLDNITP 130

Query: 141 PLFSALMKYSDIHEYSWAAPGHQGGVGFTKTPAGRFYHDYYGENLFRTDMGIERTSLGSL 200
           P   AL  Y    +Y++  PGH GG  + K+P G  ++D++G N  + D+ I  T LGSL
Sbjct: 131 PFTKALFNYVQEGKYTFCTPGHMGGSAYQKSPVGCLFYDFFGGNTLKADVSISVTELGSL 190

Query: 201 LDHTGAFGESEKYAARVFGADRSWSVVVGTSGSNRTIMQACMTDNDVVVVDRNCHKSIEQ 260
           LDH+G   E+E+Y AR FGA++S+ V  GTS SN+ +          +++DRNCHKS+  
Sbjct: 191 LDHSGPHLEAEEYIARAFGAEQSYMVTNGTSTSNKIVGMYSAPAGSTLLIDRNCHKSLAH 250

Query: 261 GLMLTGAKPVYMVPSRNRYGIIGPIYPQEMQPETLQKKISESPLTKDKAGQKPSYCVVTN 320
            LM++   P+++ P+RN  GI+G I  +E   +++Q+K++    T   AG  P + V+TN
Sbjct: 251 LLMMSDVVPLWLKPTRNALGILGGIPKREFTRDSIQQKVN----TTGGAGW-PVHAVITN 305

Query: 321 CTYDGVCYNAKEAQDLLEKTSDRLHFDEAWYGYARFNPIYADHYAMRGEPGDHNGPTVFA 380
            TYDG+ YN    ++ L+  S  +HFD AW  Y  F+PIY     M G+     G  +F 
Sbjct: 306 STYDGLLYNTTWIKETLDVPS--IHFDSAWVPYTHFHPIYQGKSGMSGDRIP--GKVIFE 361

Query: 381 THSTHKLLNALSQASYIHVREGRGAINFSRFNQAYMMHATTSPLYAICASNDVAVSMMDG 440
           T STHK+L ALSQAS IH++   G+ +   FN+A+MMH +TSP Y I AS + A +M+ G
Sbjct: 362 TQSTHKMLAALSQASLIHIK---GSYDEDTFNEAFMMHTSTSPSYPIVASIETAAAMLRG 418

Query: 441 NSGLSLTQEVIDEAVDFRQAMARLYKEFTADGSWFFKPWNKEVVTDPQTGKTYDFADAPT 500
           NSG  L Q  I+ A+DFR+ + RL +E  +DG WFF  W  E V + Q            
Sbjct: 419 NSGRRLIQRSIERALDFRKEVQRLREE--SDG-WFFDIWQPEEVGEAQ------------ 463

Query: 501 KLLTTVQDCWVMHPGESWHGFKDIPDNWSMLDPIKVSILAPGMGEDGELEETGVPAALVT 560
                   CW + PGE WHGF+D  D+   LDP+KV+IL PGM E G ++  G+PAALV 
Sbjct: 464 --------CWPVSPGEQWHGFQDADDDHMFLDPVKVTILTPGMDEQGNMDSEGIPAALVA 515

Query: 561 AWLGRHGIVPTRTTDFQIMFLFSMGVTRGKWGTLVNTLCSFKRHYDANTPLAQVMPELVE 620
            +L   G+V  +T  + ++FLFS+G+ + +   L+  L  FKR YD N  +  ++P+L  
Sbjct: 516 KFLDERGVVVEKTGPYNLLFLFSIGIDKTRAMGLLRGLTEFKRSYDLNLRVKNMLPDLYA 575

Query: 621 QYPDTYANMGIHDLGDTMFAWLKENNPGARLNEAYSGLPVAEVTPREAYNAIVDNNVELV 680
           + PD Y NM I DL   +   ++++     +  A+  LP  ++TP +A+   +   VE +
Sbjct: 576 EDPDFYRNMRIQDLAQGIHRLIRQHQLSQLMLSAFDVLPEMKMTPHQAWQRQIKGEVETI 635

Query: 681 SIENLPGRIAANSVIPYPPGIPMLLSGENFGDKNSPQVSYLRSLQSWDHHFPGFEHETEG 740
            +ENL GRI+AN ++PYPPG+P+L+ GE   +++   +++L  L S   H+PGFE +  G
Sbjct: 636 ELENLVGRISANMILPYPPGVPLLMPGEMIVEESRAVLNFLLMLCSIGRHYPGFETDIHG 695

Query: 741 TE-IIDGIYHVMCVK 754
            +   DG+Y V  +K
Sbjct: 696 AKRDEDGVYWVRVLK 710


Lambda     K      H
   0.319    0.135    0.414 

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: 1359
Number of extensions: 75
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: 755
Length of database: 712
Length adjustment: 40
Effective length of query: 715
Effective length of database: 672
Effective search space:   480480
Effective search space used:   480480
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 (21.7 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, 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