GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Pseudomonas simiae WCS417

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF4493 PS417_22995 PTS N-acetyl-D-glucosamine transporter

Query= reanno::pseudo5_N2C3_1:AO356_07335
         (954 letters)



>FitnessBrowser__WCS417:GFF4493
          Length = 836

 Score =  463 bits (1191), Expect = e-134
 Identities = 281/671 (41%), Positives = 383/671 (57%), Gaps = 23/671 (3%)

Query: 284 SARIGLANAHGLHARPAKILAQLAKSFDGEIRVRIVDGQDSAVSAKSLSKLLSLGARRGQ 343
           SA + + +  GLHARPA ++ + A+ F  + ++      D + S  SL  L+ LG   G 
Sbjct: 173 SASVRITHRGGLHARPAALIRKTAQDFSSQAQLHF---GDKSASCDSLIGLMGLGIGEGD 229

Query: 344 VLEFIAEPSIANDALPALLAAIEEGLGEEVEPLPPPSAPRETVMAEVATVMLAPESGSLI 403
            +        A  AL AL+AA+   + EE   +P  + PR            A     ++
Sbjct: 230 EVRVTCRGKDAEAALQALVAALSAVIKEE-HHVPVVAPPRR-----------AHTEAGVL 277

Query: 404 QAVAAAPGIAIGPAHIQVLQAIDYP--LRGESAAIERERLQNALNQVRSDIQGLIERAKA 461
           Q V AAPG+  GP  +  L  I+ P  +   SA  + + L  AL QVRS+I+  +  A+ 
Sbjct: 278 QGVCAAPGLVCGP--LFRLTGIELPADVGNHSADEQLQHLDTALEQVRSEIRSTLAHARQ 335

Query: 462 KAIRE---IFITHQEMLDDPELTDEVDTRLKLGESAQAAWMGVIEAAAKEQEALQDALLA 518
           +   E   IF  H  +L+DP L +     ++ G +A  AW   I+A      AL   L A
Sbjct: 336 RKNVEEEDIFAAHLALLEDPNLLEAATRSIEQGSAATHAWRDAIQAQCAVLLALGKPLFA 395

Query: 519 ERAADLRDVGRRVLAQLCGVETPNEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGGA 578
           ERA DLRD+ +RVL  L G     E     I+   E+ PSD+ +L      GI  A GGA
Sbjct: 396 ERANDLRDLQQRVLRALLGEAWHFELPAGSIVSAHELTPSDLLQLSAQHAVGICMAEGGA 455

Query: 579 TAHSAIVARALGIPALVGAGAAVLLLAPGTSLLLDGQRGRLHVDPDAATLQRAKEERDTR 638
           T+H AI+AR  G+P +V  GA VL +  G  ++LD   GRL ++P  A      + RD +
Sbjct: 456 TSHVAILARGKGLPCVVALGAEVLDVPQGQRVVLDAVNGRLELEPTEARHAEVHQIRDAQ 515

Query: 639 EQRLKVAAEQRHEPALTRDGHAVEVFANIGESAGVASAVEQGAEGIGLLRTELIFMAHSQ 698
           + R +    Q  EPA T DG ++EV AN+  SA    A E GA+G+GLLRTE +F+    
Sbjct: 516 KLRRQQQQAQAQEPARTTDGVSIEVAANVASSAEAQVAFENGADGVGLLRTEFLFVDRRT 575

Query: 699 APDEATQEAEYRKVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQR 758
           APDE  Q   Y+ VLD +  + +++RT+DVGGDK L Y P+  E NP LG+RGIR+   R
Sbjct: 576 APDEQEQRHAYQAVLDAMGDKSVIIRTIDVGGDKQLDYLPLPVEANPVLGLRGIRMAQVR 635

Query: 759 PQVMEAQLRALLRSADSRPLRIMFPMVGSVDEWRQARAMTERLRLEIPVADL-QLGIMIE 817
           P++++ QLRALL+ +     RI+ PMV  VDE  Q R   + L +E+ +    +LG+MIE
Sbjct: 636 PELLDQQLRALLQVSPLERCRILLPMVSEVDELLQIRQRLDELCVELELTQRPELGVMIE 695

Query: 818 VPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRA 877
           VP+AAL+A  LAK  DF S+GTNDL+QYTLA+DR H  L+A+ D LHPA+L+LI  T   
Sbjct: 696 VPAAALMAEHLAKHADFLSIGTNDLSQYTLAMDRDHAGLAARVDALHPALLRLIAQTCAG 755

Query: 878 AHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIAEVKARVRELSLAQVQTLAQA 937
           A  HG+WVGVCG LA+DPLA PVLVGLGV ELSVS   IAE+K RVR L  AQ + L+Q 
Sbjct: 756 ATKHGRWVGVCGALASDPLATPVLVGLGVSELSVSPPQIAEIKDRVRHLDAAQCRQLSQG 815

Query: 938 ALAVGSADDVR 948
            L + SA  VR
Sbjct: 816 LLDLSSAKAVR 826


Lambda     K      H
   0.318    0.135    0.381 

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: 1470
Number of extensions: 73
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 954
Length of database: 836
Length adjustment: 43
Effective length of query: 911
Effective length of database: 793
Effective search space:   722423
Effective search space used:   722423
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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