GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas putida KT2440

Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PP_0597 PP_0597 methylmalonate-semialdehyde dehydrogenase

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__Putida:PP_0597
          Length = 497

 Score =  898 bits (2320), Expect = 0.0
 Identities = 436/496 (87%), Positives = 470/496 (94%)

Query: 1   MTLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTP 60
           M++++HLI GEL+    RTADVFNPSTG+AVRKV LA R T+Q+AID+AKAAFPAWRNTP
Sbjct: 1   MSIVQHLIHGELVTKGERTADVFNPSTGQAVRKVELASRATVQEAIDSAKAAFPAWRNTP 60

Query: 61  PAKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKG 120
           PAKRAQV+FRFKQLLE NE +I ++ISEEHGKT+EDAAGELKRGIENVE+A AAPE+LKG
Sbjct: 61  PAKRAQVMFRFKQLLEQNEAKISQMISEEHGKTLEDAAGELKRGIENVEFACAAPEVLKG 120

Query: 121 EYSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSS 180
           EYSRNVGPNIDAWSDFQP+GVVAGITPFNFPAMVPLWMYPLAIACGN FILKPSERDPSS
Sbjct: 121 EYSRNVGPNIDAWSDFQPLGVVAGITPFNFPAMVPLWMYPLAIACGNAFILKPSERDPSS 180

Query: 181 TLLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240
           TL IA+L  EAGLPKG+LNVVHGDK AVDALIEAPEVKALSFVGSTPIAEYIY+EGTKRG
Sbjct: 181 TLYIAQLLLEAGLPKGILNVVHGDKEAVDALIEAPEVKALSFVGSTPIAEYIYAEGTKRG 240

Query: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQK 300
           KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQ+ADAL+ K
Sbjct: 241 KRVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQVADALIAK 300

Query: 301 LVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHEN 360
           L PQIK LKIGAGTSCGLDMGPLVT AARDKV GYID GVA GA+LVVDGRG++VAG+E+
Sbjct: 301 LEPQIKALKIGAGTSCGLDMGPLVTAAARDKVVGYIDDGVAAGAKLVVDGRGFRVAGNED 360

Query: 361 GFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGE 420
           G+F+GGTLFD+VTPEM IYKEEIFGPVLC+VRVNSLE+AMQLINDHEYGNGTCIFTRDGE
Sbjct: 361 GYFVGGTLFDKVTPEMRIYKEEIFGPVLCVVRVNSLEQAMQLINDHEYGNGTCIFTRDGE 420

Query: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQR 480
           AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYT+RKAITQR
Sbjct: 421 AARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTRRKAITQR 480

Query: 481 WPQRKSHEAAQFAFPS 496
           WPQR SHEA+QFAFPS
Sbjct: 481 WPQRASHEASQFAFPS 496


Lambda     K      H
   0.319    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: 882
Number of extensions: 16
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: 498
Length of database: 497
Length adjustment: 34
Effective length of query: 464
Effective length of database: 463
Effective search space:   214832
Effective search space used:   214832
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: 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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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