Alignments for a candidate for mtlD in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for mtlD in Pseudomonas putida KT2440

Align mannitol-1-phosphate 5-dehydrogenase (EC 1.1.1.17); mannitol-1-phosphatase (EC 3.1.3.22) (characterized)
to candidate PP_2052 PP_2052 putative bifunctional enzyme: sugar-phosphatase/mannitol-1-phosphate 5-dehydrogenase

Query= BRENDA::Q6FBP5
         (713 letters)



>FitnessBrowser__Putida:PP_2052
          Length = 707

 Score =  632 bits (1629), Expect = 0.0
 Identities = 329/648 (50%), Positives = 440/648 (67%), Gaps = 12/648 (1%)

Query: 1   MLIFHNYSVQGALFDMDGTMFDTERLRFQTLKQASQELLGQTFSDDYLMQCLGLSATTAE 60
           ML FH   +  A+FDMDGT+FDTERLRF+TLKQAS E+ G+  S+  L+  LGLSA  AE
Sbjct: 1   MLFFHGKQIFSAIFDMDGTLFDTERLRFRTLKQASLEIFGKALSEQTLIGSLGLSAKKAE 60

Query: 61  QLAKSQYGDDVPYKAIRKCADDLELEWVRRDGVPIKKGLVQVLERLRKSGLRMAVATSSR 120
            LAK+  G+D PY  IR+ AD+LELE+VR  GVPIK GL++VLERLRKSGL MAVATSSR
Sbjct: 61  ALAKAHNGEDFPYAQIRQRADELELEYVRNHGVPIKAGLLEVLERLRKSGLTMAVATSSR 120

Query: 121 RAIAEEYLINANVYKFFDVLVCGDEVQQGKPHPEIFEKAAQKLNLDPAQCLMFEDSENGI 180
           RAIAEEYLINANV K+FD+ VCGDEV QGKPHPEIF KAA+ LN +P QC M EDSENG+
Sbjct: 121 RAIAEEYLINANVLKYFDITVCGDEVGQGKPHPEIFLKAARALNCEPGQCFMVEDSENGM 180

Query: 181 SSAHAAGGITILLKDIKSPNEHMLSKANFYFETMYDCLLNLDDYVPIMDMPLLQETFPQT 240
            SA  A G  IL++DIK P   + + A   + +M++ L +L + VP + MP L E FP +
Sbjct: 181 LSAMRAEGQAILIEDIKPPAPEIKAGALKAYRSMHEFLADLSECVPDLGMPALSEPFPAS 240

Query: 241 LNQLTVGIHGFGAIGGGYIAQILSHWDGYTRPQRIIASTRNSLYREAVNAFGTYSIRYGQ 300
           +NQ +VGIHGFGAIGGGY+ Q+ SHWDGYTRP+ IIA+TR+ + RE+V+AFG YS+RYG 
Sbjct: 241 MNQFSVGIHGFGAIGGGYLTQVFSHWDGYTRPREIIAATRSRMLRESVSAFGRYSVRYGA 300

Query: 301 VSYDERIEYMSIIDADNEQHMLDMYLESSLIALCIPEHAVASEAKIIAKGLYARYASQTM 360
            S+D+ I+ + +ID D++  ++ MY  + +I L +PE A+ S+A++IA+GL  R+     
Sbjct: 301 TSFDQTIDNVRMIDMDDDDAVISMYTTAEIIGLSLPEQAIRSQARVIAQGLLQRFE---- 356

Query: 361 QNNNPLTFLIILNKVGAKKMVLEHIRKALENLANLEVADQIMAQHYFCDTVVNRMVSKLS 420
           +    LT LI+LNKVG    V  H++  L  L    +++Q++ + +F +TVV+R+VSKL 
Sbjct: 357 RRGRELTLLIVLNKVGGAAFVRRHVQAELSLLCPPAISEQVLQKTHFAETVVSRIVSKLG 416

Query: 421 EQNLYRQLQIKYNFFKQYQSDVDDENVEIEDTAKLSTAQEHQASLYIDDMRRNFQPSHIL 480
              L RQL+IK   F   Q+ ++DE      T K ST       L I   R   QPS  +
Sbjct: 417 NDALVRQLRIKSQMF---QNSLEDEPA---STRKSSTPLPEYERL-IGHFRPFAQPSSAM 469

Query: 481 QSMDLILFNSEIDMPIYVENNSPLLEKMRQMIVVDNIADIQLIKNRLWNGTHAMLAWYAS 540
             + L+LFNSE DMP+Y E  S LLE++RQ+  V +IA IQ+IKNRLWNG HA++AWYAS
Sbjct: 470 SQLHLVLFNSEADMPLYAERGSDLLERLRQVKTVPDIAQIQIIKNRLWNGPHAIVAWYAS 529

Query: 541 LLGHETIGVAMGDIRIQKMVNNLV-DEIKAGLATQLPHRAKDLDRLAKSFIVSCQNAYKD 599
           LLGH  +G  MGD R+ ++   L+  E+   L  + P  A+ + R A++F+  C+ ++KD
Sbjct: 530 LLGHAWVGQGMGDARVSELAERLIRQEVAPALVAEYPQMAEVVSRFAEAFLERCKTSFKD 589

Query: 600 PCQRVARDPLRKLNPNERVLGSIVNNLRYHQTVDQLLWGASLGYFYAI 647
           PC RV RDPLRKL  NER+L SI    ++      L +GA L   +A+
Sbjct: 590 PCARVGRDPLRKLQRNERILSSIDLARKHGIATPALAFGAGLAIHHAL 637


Lambda     K      H
   0.321    0.136    0.393 

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: 1062
Number of extensions: 37
Number of successful extensions: 4
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: 713
Length of database: 707
Length adjustment: 39
Effective length of query: 674
Effective length of database: 668
Effective search space:   450232
Effective search space used:   450232
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 (21.9 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