GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N1B4

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate Pf1N1B4_4277 Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4277
          Length = 500

 Score =  917 bits (2370), Expect = 0.0
 Identities = 453/500 (90%), Positives = 473/500 (94%)

Query: 1   MSDAPVVGHYLNGHVQDHDSTRFSNVFNPATGAVQARVALAEPGTVDAAVASALAAFPAW 60
           MSDA V+GHY++G VQD  S RFSNVFNPATG++QARV LA   TVD AVASAL AFPAW
Sbjct: 1   MSDAQVIGHYIDGQVQDCGSERFSNVFNPATGSIQARVGLASQKTVDDAVASALKAFPAW 60

Query: 61  SEQSSLRRSRVMFKFKELLDRHHDELAQIISREHGKVLSDAHGEVTRGIEIVEYACGAPN 120
           SEQSSLRRSRVMFKFKELLDRHH+ELA+IISREHGKV SDA GEVTRGIEIVEYACGAPN
Sbjct: 61  SEQSSLRRSRVMFKFKELLDRHHNELAEIISREHGKVFSDAKGEVTRGIEIVEYACGAPN 120

Query: 121 LLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVAGNCFILKPSER 180
           LLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALV GNCFILKPSER
Sbjct: 121 LLKTDFSDNIGGGIDNWNLRQPLGVCAGVTPFNFPVMVPLWMIPLALVTGNCFILKPSER 180

Query: 181 DPSASLLMARLLTEAGLPDGVFNVVQGDKVAVDALLQHPDIEAISFVGSTPIAEYIHQQG 240
           DPSASLLMA+LLTEAGLPDGVFNVVQGDK AVDALLQHPDIEAISFVGSTPIAEYIHQQ 
Sbjct: 181 DPSASLLMAKLLTEAGLPDGVFNVVQGDKAAVDALLQHPDIEAISFVGSTPIAEYIHQQA 240

Query: 241 TAHGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVAVGDVGDEL 300
           T+ GKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAV VGDVGD+L
Sbjct: 241 TSRGKRVQALGGAKNHMIVMPDADLDQAADALIGAAYGSAGERCMAISIAVTVGDVGDQL 300

Query: 301 IAKLLPRIDQLKIGNGQQPGTDMGPLVTAEHKAKVEGFIDAGVAEGARLIVDGRSFKVPG 360
           IAKLLPRIDQLK+GNG Q  +DMGPLVTAEHKAKVEGFI  GVA+GA+LIVDGR+FKVPG
Sbjct: 301 IAKLLPRIDQLKVGNGMQGDSDMGPLVTAEHKAKVEGFIGEGVAQGAQLIVDGRNFKVPG 360

Query: 361 AEQGFFVGATLFDQVTAEMSIYQQEIFGPVLGIVRVPDFATAVALINAHEFGNGVSCFTR 420
           AE GFFVGATLFD VT EMSIYQQEIFGPVLGIVRVPDFA+AVALINAHEFGNGVSCFT 
Sbjct: 361 AENGFFVGATLFDNVTTEMSIYQQEIFGPVLGIVRVPDFASAVALINAHEFGNGVSCFTS 420

Query: 421 DGGIARAFARSIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGLRFYSRYKSV 480
           DGGIAR+FAR+IKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEG+RFYSRYKSV
Sbjct: 421 DGGIARSFARNIKVGMVGINVPIPVPMAWHSFGGWKRSLFGDHHAYGEEGIRFYSRYKSV 480

Query: 481 MQRWPDSIAKGPEFSMPTAQ 500
           MQRWPDSIAKGPEFSMPTA+
Sbjct: 481 MQRWPDSIAKGPEFSMPTAK 500


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: 877
Number of extensions: 23
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: 500
Length adjustment: 34
Effective length of query: 466
Effective length of database: 466
Effective search space:   217156
Effective search space used:   217156
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