GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Acidovorax sp. GW101-3H11

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 Ac3H11_4340 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::A0A081YAY7
         (498 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4340
          Length = 505

 Score =  723 bits (1867), Expect = 0.0
 Identities = 353/496 (71%), Positives = 408/496 (82%)

Query: 2   TLIKHLIGGELIADTGRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPP 61
           T + HLI G+ +AD  RT  VFNP+TG++   V LA + T++ AI +A+AAFPAWRNTPP
Sbjct: 9   TTVGHLIDGKSVADAERTQPVFNPATGQSTTSVALASKATVEAAIASAEAAFPAWRNTPP 68

Query: 62  AKRAQVLFRFKQLLEANEERIVKLISEEHGKTIEDAAGELKRGIENVEYATAAPEILKGE 121
            KRA+V+ + K LLE N ++I  LI+ EHGK + DA GEL+RGIENVEYA+ APE+LKGE
Sbjct: 69  LKRARVMSKLKVLLEENADKIAALITAEHGKVLADAHGELQRGIENVEYASYAPELLKGE 128

Query: 122 YSRNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSST 181
           +SRNVGP+ID+WS+FQ +GV AGITPFNFPAMVPLWM+P+A+ACGNTF+LKPSERDPSST
Sbjct: 129 HSRNVGPSIDSWSEFQALGVTAGITPFNFPAMVPLWMWPMAVACGNTFVLKPSERDPSST 188

Query: 182 LLIAELFHEAGLPKGVLNVVHGDKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRGK 241
           L IA+L  EAGLP GVLNVV+GDK AVD L++ P VKA+SFVGSTPIAEYIYSEG K GK
Sbjct: 189 LFIAQLALEAGLPPGVLNVVNGDKLAVDTLLQDPRVKAVSFVGSTPIAEYIYSEGCKHGK 248

Query: 242 RVQALGGAKNHAVLMPDADLDNAVSALMGAAYGSCGERCMAISVAVCVGDQIADALVQKL 301
           RVQALGGAKNHAVLMPDAD+ NAVSALMGAAYGSCGERCMAI + V VGD + DA++  L
Sbjct: 249 RVQALGGAKNHAVLMPDADVGNAVSALMGAAYGSCGERCMAIPLLVAVGDAVGDAVIAGL 308

Query: 302 VPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKVAGHENG 361
             +I  +K+G GT    DMGPLVT    +KV  Y+D+GV +GA LVVDGRG KVAGHE G
Sbjct: 309 KTEIAKMKVGPGTDNSNDMGPLVTKPHFEKVKAYVDSGVTEGATLVVDGRGVKVAGHEEG 368

Query: 362 FFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCIFTRDGEA 421
           +FLG  LFD V P M IY+EEIFGPVL +VRV +L+EAMQLINDHEYGNGTCIFTRDGEA
Sbjct: 369 YFLGACLFDNVKPGMKIYQEEIFGPVLGVVRVKTLQEAMQLINDHEYGNGTCIFTRDGEA 428

Query: 422 ARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDGVRFYTKRKAITQRW 481
           AR F D I+VGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPD VRFYTKRK ITQRW
Sbjct: 429 ARYFTDHIQVGMVGVNVPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTITQRW 488

Query: 482 PQRKSHEAAQFAFPSN 497
           P     E A F+FPS+
Sbjct: 489 PSAGVREGAVFSFPSS 504


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: 828
Number of extensions: 20
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: 505
Length adjustment: 34
Effective length of query: 464
Effective length of database: 471
Effective search space:   218544
Effective search space used:   218544
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