GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Pseudomonas putida KT2440

Align L-lactate dehydrogenase [cytochrome]; EC 1.1.2.3 (characterized)
to candidate PP_4736 PP_4736 L-lactate dehydrogenase

Query= CharProtDB::CH_000618
         (396 letters)



>FitnessBrowser__Putida:PP_4736
          Length = 381

 Score =  652 bits (1682), Expect = 0.0
 Identities = 322/380 (84%), Positives = 348/380 (91%)

Query: 1   MIISAASDYRAAAQRILPPFLFHYMDGGAYSEYTLRRNVEDLSEVALRQRILKNMSDLSL 60
           MIISA++DYRAAAQR LPPFLFHY DGGAY+E+TLR NV DL+ +ALRQR+L NMS+LSL
Sbjct: 1   MIISASTDYRAAAQRKLPPFLFHYADGGAYAEHTLRHNVSDLAGIALRQRVLNNMSELSL 60

Query: 61  ETTLFNEKLSMPVALAPVGLCGMYARRGEVQAAKAADAHGIPFTLSTVSVCPIEEVAPAI 120
           ET LF+E LSMPVALAPVGL GMYARRGEVQAA+AA AHGIPFT+STVSVCPIEEVAPAI
Sbjct: 61  ETKLFDETLSMPVALAPVGLTGMYARRGEVQAARAAAAHGIPFTMSTVSVCPIEEVAPAI 120

Query: 121 KRPMWFQLYVLRDRGFMRNALERAKAAGCSTLVFTVDMPTPGARYRDAHSGMSGPNAAMR 180
            RPMWFQLYVL+DRGFMRNALERAKAAG  TLVFTVDMP PGARYRDAHSGMSG N  +R
Sbjct: 121 NRPMWFQLYVLKDRGFMRNALERAKAAGVKTLVFTVDMPVPGARYRDAHSGMSGKNGPLR 180

Query: 181 RYLQAVTHPQWAWDVGLNGRPHDLGNISAYLGKPTGLEDYIGWLGNNFDPSISWKDLEWI 240
           R LQA+THP+WAWDVG+ GRPHDLGNIS Y G PTGL DYIGWLGNNFDPSISWKDLEWI
Sbjct: 181 RVLQAMTHPEWAWDVGVMGRPHDLGNISKYRGNPTGLADYIGWLGNNFDPSISWKDLEWI 240

Query: 241 RDFWDGPMVIKGILDPEDARDAVRFGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGD 300
           R+FWDGPM+IKGILD +DARDAV+FGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGD
Sbjct: 241 REFWDGPMIIKGILDADDARDAVKFGADGIVVSNHGGRQLDGVLSSARALPAIADAVKGD 300

Query: 301 IAILADSGIRNGLDVVRMIALGADTVLLGRAFLYALATAGQAGVANLLNLIEKEMKVAMT 360
           + ILADSGIR+GLDVVRMIALGADTVL+GRAFLYALA  GQAGV NLL L EKEM+VAM 
Sbjct: 301 LKILADSGIRSGLDVVRMIALGADTVLIGRAFLYALAVHGQAGVKNLLELFEKEMRVAMV 360

Query: 361 LTGAKSISEITQDSLVQGLG 380
           LTGAKSISEIT+DSLV+ LG
Sbjct: 361 LTGAKSISEITRDSLVRELG 380


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: 572
Number of extensions: 14
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 396
Length of database: 381
Length adjustment: 30
Effective length of query: 366
Effective length of database: 351
Effective search space:   128466
Effective search space used:   128466
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: 50 (23.9 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:

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:

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:

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:

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