GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Paraburkholderia bryophila 376MFSha3.1

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate H281DRAFT_03264 H281DRAFT_03264 methylmalonate-semialdehyde dehydrogenase [acylating]

Query= reanno::pseudo6_N2E2:Pf6N2E2_515
         (500 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03264 H281DRAFT_03264
           methylmalonate-semialdehyde dehydrogenase [acylating]
          Length = 507

 Score =  756 bits (1951), Expect = 0.0
 Identities = 366/494 (74%), Positives = 417/494 (84%), Gaps = 1/494 (0%)

Query: 7   VGHYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSL 66
           +GHY+ G   D  S RF  VFNPATG V   VALA    VDAAV SA AAF AWSE + L
Sbjct: 15  IGHYIGGVAVDPASGRFKEVFNPATGQVTGAVALASIEEVDAAVQSAKAAFAAWSETAPL 74

Query: 67  RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDF 126
           +R+R++FKFKELL++HHDELA +I+REHGKV +DA GEV RGIE+VE+ACG PNLLKTDF
Sbjct: 75  KRARILFKFKELLNKHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDF 134

Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186
           +D IGGGIDNWNLRQPLGV AG+TPFNFPVMVP+WM P+AL  GN F+LKPSERDPSASL
Sbjct: 135 TDQIGGGIDNWNLRQPLGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASL 194

Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAHGKR 246
            +A LL EAGLPDGVFNVV GDKVAVDAL++HPD+ A+SFVGSTPIAEYIH + +  GKR
Sbjct: 195 RIAELLKEAGLPDGVFNVVNGDKVAVDALIEHPDVAALSFVGSTPIAEYIHTEASKRGKR 254

Query: 247 VQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLP 306
           VQALGGAKNH++VMPDADLDQA DALIGAAYGSAGERCMAIS+AVAVG+V D+LI KL+P
Sbjct: 255 VQALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGNVADKLIEKLVP 314

Query: 307 RIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFF 366
           R+  L I NG+    +MGPLVTAEHKAKV G+I +G  EGA LIVDGR+  V   E GFF
Sbjct: 315 RVKSLVIKNGENLDAEMGPLVTAEHKAKVAGYIASGEEEGATLIVDGRAHPVAN-EAGFF 373

Query: 367 VGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIAR 426
           +G TLFD V  +M IY++EIFGPVL +VRVPDFA+AV LINAHEFGNGVS FT DGG+AR
Sbjct: 374 IGGTLFDNVGTQMKIYKEEIFGPVLAVVRVPDFASAVELINAHEFGNGVSLFTSDGGVAR 433

Query: 427 AFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPD 486
           AF R I+VGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEG+RFY+RYKS+MQRWPD
Sbjct: 434 AFGRQIQVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGVRFYTRYKSIMQRWPD 493

Query: 487 SIAKGPEFSMPTAQ 500
           SIAKG EF+MP A+
Sbjct: 494 SIAKGAEFTMPVAK 507


Lambda     K      H
   0.321    0.137    0.415 

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: 823
Number of extensions: 30
Number of successful extensions: 2
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: 500
Length of database: 507
Length adjustment: 34
Effective length of query: 466
Effective length of database: 473
Effective search space:   220418
Effective search space used:   220418
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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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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