GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_03264
          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:

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