GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Burkholderia phytofirmans PsJN

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate BPHYT_RS28825 BPHYT_RS28825 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo5_N2C3_1:AO356_23175
         (500 letters)



>FitnessBrowser__BFirm:BPHYT_RS28825
          Length = 507

 Score =  756 bits (1953), Expect = 0.0
 Identities = 366/494 (74%), Positives = 419/494 (84%), Gaps = 1/494 (0%)

Query: 7   VGHYIDGRIQASDNARLSNVFNPATGAVQARVALAEPSTVDAAVASALAAFPAWSEQSSL 66
           +GHYI G   A  + R  +VFNPATG V   VALA    VDAAV +A AAFPAWSE + L
Sbjct: 15  LGHYIGGAPAAPTSGRFKDVFNPATGKVTGSVALASVEEVDAAVQAARAAFPAWSETAPL 74

Query: 67  RRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDF 126
           +R+R++F+FKELL++HHDELA +I+REHGKV +DA GEV RGIE+VE+ACG PNLLKTDF
Sbjct: 75  KRARILFRFKELLNQHHDELAMLITREHGKVFTDAQGEVVRGIEVVEFACGIPNLLKTDF 134

Query: 127 SDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASL 186
           +D IGGGIDNWNLRQ LGV AG+TPFNFPVMVP+WM P+AL  GN F+LKPSERDPSASL
Sbjct: 135 TDQIGGGIDNWNLRQALGVVAGITPFNFPVMVPMWMFPVALACGNTFVLKPSERDPSASL 194

Query: 187 LMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAQGKR 246
            +A LL EAGLPDGVFNVV GDKVAVDAL+ HPD+ A+SFVGSTPIAEYIH + + +GKR
Sbjct: 195 RLAELLKEAGLPDGVFNVVNGDKVAVDALIDHPDVAALSFVGSTPIAEYIHTEASKRGKR 254

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

Query: 307 RIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRGFKVPGAEQGFF 366
           R+  L I NG+    +MGPLVTAEHKAKV G+I +G AEGA+LIVDGR   V   E+GFF
Sbjct: 315 RVKSLVIKNGEHLDAEMGPLVTAEHKAKVTGYIASGEAEGAKLIVDGRAHPVTN-EEGFF 373

Query: 367 VGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIAR 426
           VG TLFD V  EM IY++EIFGPVL +VRVPDFA+AV LINAHEFGNGVS FT DGG+AR
Sbjct: 374 VGGTLFDHVGTEMKIYKEEIFGPVLAVVRVPDFASAVDLINAHEFGNGVSLFTSDGGVAR 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
   0.320    0.137    0.412 

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: 816
Number of extensions: 27
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.

Links

Downloads

Related tools

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