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_02373 H281DRAFT_02373 methylmalonate-semialdehyde dehydrogenase [acylating]

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



>FitnessBrowser__Burk376:H281DRAFT_02373
          Length = 512

 Score =  767 bits (1980), Expect = 0.0
 Identities = 364/492 (73%), Positives = 423/492 (85%)

Query: 9   HYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAWSEQSSLRR 68
           H++NG   D  S RF +VFNPA G V ARV LA    VDAAVA+A AAFPAWSE + ++R
Sbjct: 21  HFINGKAIDGTSGRFGDVFNPALGDVAARVPLASVAEVDAAVAAAYAAFPAWSETAPIKR 80

Query: 69  SRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPNLLKTDFSD 128
           +RV+FKFKELLDRHHDELA++I+REHGKV SDA GEV RGIE+VE+ACG PNLLKTDF+D
Sbjct: 81  ARVLFKFKELLDRHHDELAELITREHGKVFSDAKGEVMRGIEVVEFACGIPNLLKTDFTD 140

Query: 129 NIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSERDPSASLLM 188
            IGGGIDNWNLRQPLGV  G+TPFNFP+MVP WM P+A+  GN F+LKPSERDPSAS  +
Sbjct: 141 QIGGGIDNWNLRQPLGVVVGITPFNFPMMVPCWMFPVAIACGNTFVLKPSERDPSASNRL 200

Query: 189 ARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQGTAHGKRVQ 248
           A LL EAGLPDGVFNVV GDKVAVDALL HPD+ A+SFVGSTPIAEYIH +GT HGKRVQ
Sbjct: 201 AELLKEAGLPDGVFNVVHGDKVAVDALLVHPDVSAVSFVGSTPIAEYIHTEGTKHGKRVQ 260

Query: 249 ALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDELIAKLLPRI 308
           ALGGAKNH++VMPDADLDQA DALIGAAYGSAGERCMAIS+AVAVG + DELI +L PR+
Sbjct: 261 ALGGAKNHLVVMPDADLDQAVDALIGAAYGSAGERCMAISVAVAVGHIADELIERLTPRV 320

Query: 309 DQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPGAEQGFFVG 368
           + LKI NG +   +MGPLVTA H+ KV G+I+AG+AEGA+L+VDGR  +V G E+GFF+G
Sbjct: 321 ESLKIMNGMESAAEMGPLVTAVHREKVVGYIEAGIAEGAKLVVDGRGHRVDGHEKGFFLG 380

Query: 369 ATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTRDGGIARAF 428
            TLFD V+ +M IY++EIFGPVL +VRVPDFA+AV LINA++F NGVS FT DGGIARAF
Sbjct: 381 GTLFDDVSTDMKIYREEIFGPVLCVVRVPDFASAVELINANDFANGVSLFTSDGGIARAF 440

Query: 429 ARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSVMQRWPDSI 488
           +R I++GMVGINVPIPVPMAWHSFGGWK+SLFGDHHAYGEEG+RFY+RYKS+MQRWPDSI
Sbjct: 441 SRQIQIGMVGINVPIPVPMAWHSFGGWKKSLFGDHHAYGEEGVRFYTRYKSIMQRWPDSI 500

Query: 489 AKGPEFSMPTAQ 500
           AKG EF+MP A+
Sbjct: 501 AKGAEFTMPVAK 512


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: 849
Number of extensions: 32
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: 500
Length of database: 512
Length adjustment: 34
Effective length of query: 466
Effective length of database: 478
Effective search space:   222748
Effective search space used:   222748
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