Aligments for a candidate for liuD in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for liuD in Pseudomonas putida KT2440

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate PP_4065 PP_4065 methylcrotonyl-CoA carboxylase biotin-containing subunit beta

Query= reanno::pseudo6_N2E2:Pf6N2E2_2192
         (535 letters)



>lcl|FitnessBrowser__Putida:PP_4065 PP_4065 methylcrotonyl-CoA
           carboxylase biotin-containing subunit beta
          Length = 535

 Score =  990 bits (2560), Expect = 0.0
 Identities = 490/535 (91%), Positives = 508/535 (94%)

Query: 1   MATLHTQLNPRSPEFIANRDAMLGHVEALRTLLAQIRQGGGPKAQERHTSRGKLLPRERI 60
           MATLHTQ+NPRS EF  N  AML  V+ALR LLAQ+ QGGGPKAQERHTSRGKLLPRERI
Sbjct: 1   MATLHTQINPRSAEFAVNSAAMLEQVQALRGLLAQVAQGGGPKAQERHTSRGKLLPRERI 60

Query: 61  NRLLDPGSPFLEISPLAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120
           +RLLDPGSPFLEI  LAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL
Sbjct: 61  DRLLDPGSPFLEIGQLAAHEVYGEDVPAAGVIAGIGRVEGVECMIVANDATVKGGSYYPL 120

Query: 121 TVKKHLRAQTIAQQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180
           TVKKHLRAQTIA QNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ
Sbjct: 121 TVKKHLRAQTIALQNRLPCIYLVDSGGANLPRQDEVFPDREHFGRIFFNQANMSAQGIPQ 180

Query: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCK 240
           IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHC+
Sbjct: 181 IAVVMGSCTAGGAYVPAMADEAIMVRQQATIFLAGPPLVKAATGEVVSAEDLGGADVHCR 240

Query: 241 ISGVADHYADSDEHALALARRSVANLNWRKQGELQHRLPIAPLYSGEELYGVVSADAKQP 300
            SGVADHYAD+DEHALA+ARRSVANLNW K G+LQ   P+APLY+ +ELYGVV ADAKQP
Sbjct: 241 TSGVADHYADNDEHALAIARRSVANLNWHKLGKLQRLAPVAPLYAADELYGVVPADAKQP 300

Query: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPIAILANNGILFAEAAQKGAHFI 360
           FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYP+AILANNGILFAEAAQKGAHFI
Sbjct: 301 FDVREVIARLVDGSVFDEFKALFGTTLVCGFAHLHGYPVAILANNGILFAEAAQKGAHFI 360

Query: 361 ELACQRGIPLLFLQNITGFMVGQKYEAGGIAKHGAKLVTAVACAKVPKFTVIIGGSFGAG 420
           ELACQRGIPLLFLQNITGFMVG+KYE GGIAKHGAKLVTAVACA+VPKFTVIIGGSFGAG
Sbjct: 361 ELACQRGIPLLFLQNITGFMVGKKYEEGGIAKHGAKLVTAVACAQVPKFTVIIGGSFGAG 420

Query: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLVQVKREQAERSGHPFSAEQEAEIKQP 480
           NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVL QVKREQ+ERSG PFSAE EA +KQP
Sbjct: 421 NYGMCGRAYDPRFLWMWPNARIGVMGAEQAAGVLAQVKREQSERSGQPFSAEDEARLKQP 480

Query: 481 ILDQYEEQGHPYYSSARLWDDGVIDPAQTRDVLGLALSASLNAPIEPSRFGVFRM 535
           ILDQYE QGHPYYSSARLWDDGVIDPAQTRDVLGLALSA+LNAPIE SRFG+FRM
Sbjct: 481 ILDQYERQGHPYYSSARLWDDGVIDPAQTRDVLGLALSAALNAPIEQSRFGIFRM 535


Lambda     K      H
   0.321    0.137    0.411 

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: 1120
Number of extensions: 34
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: 535
Length of database: 535
Length adjustment: 35
Effective length of query: 500
Effective length of database: 500
Effective search space:   250000
Effective search space used:   250000
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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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 preprint 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