GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Pseudomonas fluorescens GW456-L13

Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate PfGW456L13_926 glutamine synthetase family protein

Query= reanno::MR1:200446
         (451 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_926
          Length = 452

 Score =  687 bits (1773), Expect = 0.0
 Identities = 329/451 (72%), Positives = 385/451 (85%), Gaps = 3/451 (0%)

Query: 1   MNKLIAFLKERKITEVECVICDMTGIARGKIAPVDKFLDEKGMRLPESVLLQTVTGDFVD 60
           +++L  +LK  KITEVEC+I D+TGI RGKI+P +KF+ EKGMRLPESVLLQTVTGD+V+
Sbjct: 5   LDQLTDWLKNHKITEVECMIADLTGITRGKISPTNKFIAEKGMRLPESVLLQTVTGDYVE 64

Query: 61  DDIYYSLLDDADIDFVCVPDENAVFMLPWTIEATAQVIHDCYDRMGNPIELSPRNVLKKV 120
           DDIYY LLD ADID +C PD++AV+++PW IE TA VIHD YD+ GNPIELSPRNVLKKV
Sbjct: 65  DDIYYELLDPADIDMICRPDQSAVYLVPWAIEPTAIVIHDTYDKQGNPIELSPRNVLKKV 124

Query: 121 LSLYDEKGWEPVIAPEMEFYLTSRSDDHDLPLKPPIGRSGRPEAGRQSFSIDAANEYDPL 180
           L LY +KGW+P++APEMEFYLT RSDD D PL+PPIGRSGRPE GRQSFSI+AANE+DPL
Sbjct: 125 LKLYTDKGWQPIVAPEMEFYLTKRSDDPDYPLQPPIGRSGRPEIGRQSFSIEAANEFDPL 184

Query: 181 FEDMYDWCEIQGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVC 240
           FED+YDWCE+Q LD+DTLIHEDG AQMEINF HG+ LSLADQ+ VFKRT+REAALKH+V 
Sbjct: 185 FEDVYDWCELQDLDLDTLIHEDGTAQMEINFRHGDALSLADQILVFKRTMREAALKHDVA 244

Query: 241 ATFMAKPVTDEPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPL 300
           ATFMAKP+T EPGSAMH+HQSVI+ ETGKNIF+NEDGT S LFL +I GLQK IPE LPL
Sbjct: 245 ATFMAKPMTGEPGSAMHLHQSVIDIETGKNIFSNEDGTMSQLFLHHIGGLQKLIPELLPL 304

Query: 301 MAPNANSFRRFLPGTSAPVNLEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFA 360
            APN NSFRRFLP TSAPVN+EWG ENRT GLR+P++ PQNRR+ENR+PGADAN YLA A
Sbjct: 305 FAPNVNSFRRFLPDTSAPVNVEWGEENRTVGLRVPDAGPQNRRVENRLPGADANPYLAIA 364

Query: 361 AGLLCGYIGMVEGLKPSTPVQGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESF 420
           A LLCGYIGMVEGL PS PV G+  E R+     LPLT+E+AL  ME S   ++YLG++F
Sbjct: 365 ASLLCGYIGMVEGLNPSAPVVGRGYERRNLR---LPLTIEDALERMEHSSTIEKYLGKNF 421

Query: 421 TTGFVAVKQAELENFRRVVSSWEREFLLLSV 451
            TG+VAVK+AE ENF+RV+SSWEREFLL +V
Sbjct: 422 ITGYVAVKRAEHENFKRVISSWEREFLLFAV 452


Lambda     K      H
   0.319    0.137    0.414 

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: 711
Number of extensions: 23
Number of successful extensions: 3
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: 451
Length of database: 452
Length adjustment: 33
Effective length of query: 418
Effective length of database: 419
Effective search space:   175142
Effective search space used:   175142
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 (21.7 bits)
S2: 51 (24.3 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