GapMind for catabolism of small carbon sources

 

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

Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate Pf1N1B4_4826 glutamine synthetase family protein

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4826
          Length = 452

 Score =  667 bits (1722), Expect = 0.0
 Identities = 322/450 (71%), Positives = 376/450 (83%), Gaps = 3/450 (0%)

Query: 2   NKLIAFLKERKITEVECVICDMTGIARGKIAPVDKFLDEKGMRLPESVLLQTVTGDFVDD 61
           ++L  +LK+ KITEVECV+ D+TGIARGKIAP +KFL E+GMRLPESVLLQTVTGDFVDD
Sbjct: 6   DQLFTWLKDHKITEVECVVSDLTGIARGKIAPTNKFLHERGMRLPESVLLQTVTGDFVDD 65

Query: 62  DIYYSLLDDADIDFVCVPDENAVFMLPWTIEATAQVIHDCYDRMGNPIELSPRNVLKKVL 121
           DIYY LLD ADID VC P  +AV+++PW IE TA VIHD +D+ GNPIELSPRNVLKKVL
Sbjct: 66  DIYYDLLDPADIDMVCKPVADAVYVIPWAIEPTAIVIHDTFDKFGNPIELSPRNVLKKVL 125

Query: 122 SLYDEKGWEPVIAPEMEFYLTSRSDDHDLPLKPPIGRSGRPEAGRQSFSIDAANEYDPLF 181
            LY +KGW+P++APEMEFYLT R +D DLPLK P+GRSGR E+GRQSFSIDAANE+DPLF
Sbjct: 126 QLYTDKGWKPIVAPEMEFYLTQRCEDPDLPLKAPLGRSGRAESGRQSFSIDAANEFDPLF 185

Query: 182 EDMYDWCEIQGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVCA 241
           ED+YDWCE+QGLD+DTLIHEDGPAQMEINF HG+ L LADQ+ VFKRTLREAALKHNV A
Sbjct: 186 EDVYDWCELQGLDLDTLIHEDGPAQMEINFRHGDALDLADQITVFKRTLREAALKHNVTA 245

Query: 242 TFMAKPVTDEPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPLM 301
           TFMAKP+ DEPGSAMH+HQSV++  TG+ IF + DG  S LFL +I GLQKYIP+ LP+ 
Sbjct: 246 TFMAKPIGDEPGSAMHLHQSVVDIATGQPIFADADGQMSELFLHHIGGLQKYIPKVLPMF 305

Query: 302 APNANSFRRFLPGTSAPVNLEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFAA 361
           APN NSFRRFLP TSAPVN+EWG ENRT GLR+P SSP   R+ENR+PGADAN YLA AA
Sbjct: 306 APNVNSFRRFLPDTSAPVNVEWGEENRTVGLRVPTSSPDAMRVENRLPGADANPYLAIAA 365

Query: 362 GLLCGYIGMVEGLKPSTPVQGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESFT 421
            LLCGY+GMVE ++PS  VQG+A E R+     LP+T+E+AL  MEE +  + YLG  F 
Sbjct: 366 SLLCGYLGMVEKVEPSAAVQGRAYERRNLR---LPITIEDALTRMEECETIERYLGSKFV 422

Query: 422 TGFVAVKQAELENFRRVVSSWEREFLLLSV 451
            G+VAVK+AE ENF+RV+SSWEREFLLLSV
Sbjct: 423 RGYVAVKRAEHENFKRVISSWEREFLLLSV 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: 695
Number of extensions: 20
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: 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