GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat in Pseudomonas fluorescens FW300-N2E2

Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate Pf6N2E2_5326 Acetylornithine aminotransferase (EC 2.6.1.11)

Query= BRENDA::A4F7V1
         (447 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5326
          Length = 396

 Score =  138 bits (348), Expect = 3e-37
 Identities = 132/433 (30%), Positives = 204/433 (47%), Gaps = 45/433 (10%)

Query: 17  DAVTSLKAQVTGDLMDIVVDLDAGDGCRLRDLRDGTEYLDMTMFFSSATLGHGHPGLRTP 76
           DA+T+     T     + +    G G RL D +DG EYLD     +   +GH HP L   
Sbjct: 4   DAMTAACLMTT--YQPLALSFTHGLGTRLWD-QDGREYLDAVAGVAVTNVGHSHPRL--- 57

Query: 77  EFEAALVRAGRVKPSNPDFATVEQARFAETFRRVAGDPQLPLLFFIDGGTLAVENALKVA 136
              A   +AG +  ++  ++   Q R A+   +++G   L   FF + G  A E ALK+A
Sbjct: 58  -VAAISEQAGLLLHTSNLYSIDWQQRLAQKLTQLSG---LERAFFNNSGAEANETALKLA 113

Query: 137 --FDWKTKVNARKGVAIRGSRVLHLEKAFHGRSGYTLSLTNTDPSKIRDYPMFDWPRIPS 194
             + W       KG  I    V+ ++ AFHGR+  T+  +  D   +R      + R+P 
Sbjct: 114 RLYGW------HKG--IEQPLVVVMDNAFHGRTLGTMCAS--DGPSVR----LGFNRLPG 159

Query: 195 PAV-VPGDDWDDPELLPHERVAVEAAEAALRRYGREIACFVYEPIQGEGGDRHLRPRFLR 253
             + VP  D             + A EA  + +   I   + EPIQGE G +   P +L+
Sbjct: 160 DFIKVPFGD-------------LAALEAIQQAHAERIVAVLVEPIQGESGVQLAPPGYLK 206

Query: 254 AVQELCREHDVLTVADEVQTG-ALTGRAWAYQALGLEPDLVAFGKRMQVCGVMGGRRVLE 312
           A++ELC     L + DE+QTG   TG+ +A+Q  G+ PD++   K +     +G      
Sbjct: 207 ALRELCSRRAWLLMLDEIQTGIGRTGQWFAFQHEGIVPDVMTLAKGLGNGVPIGACLARG 266

Query: 313 VEENAFREASRISSTWGGSLTDMVRATRILEVIESEDLFEHSRQMGELLLGELRALVAEF 372
                F   S  S+  G  L   V  T +LE+IE + L +++R  G+ LLG LR  +A+ 
Sbjct: 267 KAAELFTPGSHGSTFGGNPLACRVGCT-VLEIIEQQALVDNARHQGDQLLGRLRIELADN 325

Query: 373 PSVVRDARGRGLMCAISFADPDKRNRALAVARDHHRTLFLPSGTDSLRCRPPLSVRPEEV 432
           P+V+   RG+GLM  I    P  R+ AL  ARDH   + +  G  ++R  PPL++   EV
Sbjct: 326 PNVLA-IRGQGLMIGIELKQP-VRDLALRAARDHGLLINITRG-QTIRLLPPLTIDGREV 382

Query: 433 VDAVSALRKTLVE 445
              V  + + L +
Sbjct: 383 EMIVRGVSRCLAQ 395


Lambda     K      H
   0.321    0.137    0.410 

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: 421
Number of extensions: 22
Number of successful extensions: 4
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: 447
Length of database: 396
Length adjustment: 32
Effective length of query: 415
Effective length of database: 364
Effective search space:   151060
Effective search space used:   151060
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 (21.9 bits)
S2: 50 (23.9 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