GapMind for catabolism of small carbon sources

 

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

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Pf1N1B4_2284 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2284
          Length = 759

 Score =  296 bits (759), Expect = 2e-84
 Identities = 197/576 (34%), Positives = 307/576 (53%), Gaps = 39/576 (6%)

Query: 279 GVCASAGSAFGYVVQ---------VAERTLEMPEFAADQQLERESLE--RALMHATQALQ 327
           GV  S G+A G  V          V ++T+   +  A+  L + ++E  RA M A  A  
Sbjct: 180 GVPGSPGAAVGTAVVMLPPADLDVVPDKTIT--DINAELGLFKTAIEGVRADMRALSA-- 235

Query: 328 RLRDNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLG 387
           +L      E +A +F  +  +L+D SL  +   +I  G+ A  A           F+ + 
Sbjct: 236 KLATQLRPEERA-LFDVYLMMLDDASLGSEITTVIKTGQWAQGALRQVVTEHVNRFELMD 294

Query: 388 STLLAERALDLMDVGQRVLKLILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFA 447
              L ERA D+ D+G+R+L  +          PD  IL++E+LTP+    +  GK++G  
Sbjct: 295 DAYLRERASDVKDLGRRLLAYLQEERQQTLVYPDNTILVSEELTPAMLGEVPEGKLVGLV 354

Query: 448 TVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLH 507
           +V G   SHVAILARA+G+P V GL     S   G ++++D   GE++ +P+  + +Q  
Sbjct: 355 SVLGSGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFA 414

Query: 508 AKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFL 567
              ++++Q             VT DGH   +  N   LA+  +A   GAEG+GL R+E  
Sbjct: 415 EVVEEEKQLALGLDALRDLPCVTVDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVP 474

Query: 568 YQQRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRG 627
           +      PS  EQ   Y     A  PQ  + +R+LD+GGDK L+Y P+  E NPFLG RG
Sbjct: 475 FMINQRFPSEKEQLAIYREQLAAFHPQP-VTMRSLDIGGDKALSYFPI-KEDNPFLGWRG 532

Query: 628 IRLCLERPQLLREQFRAIL-SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRE- 685
           IR+ L+ P++   Q RA+L +S GL  L I+LPM+S + EL        EEAL L  R  
Sbjct: 533 IRVTLDHPEIFLVQTRAMLKASEGLNNLRILLPMISGIHEL--------EEALHLIHRAW 584

Query: 686 -----------LPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLA 734
                      +P +G+MIE+PAA       A +VDF S+G+NDLTQY LA+DR++PR+A
Sbjct: 585 GEVRDEGTDVPMPPVGVMIEIPAAVYQTRELARQVDFLSVGSNDLTQYLLAVDRNNPRVA 644

Query: 735 SQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIP 794
              D  HP+VL+ + + V+ AHA GK V +CG +A +  A  LL+ +G D LS++   +P
Sbjct: 645 DLYDYLHPAVLQALQNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLP 704

Query: 795 AIKAAIREVELSDCQAIAHQVLGLESAEQVREALSV 830
            +K  +R++ LS  + +  +++ +++ + +  +L +
Sbjct: 705 KVKWMLRQINLSKAKELLAELMTIDNPQVIHSSLQL 740


Lambda     K      H
   0.318    0.132    0.370 

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: 1244
Number of extensions: 59
Number of successful extensions: 7
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: 844
Length of database: 759
Length adjustment: 41
Effective length of query: 803
Effective length of database: 718
Effective search space:   576554
Effective search space used:   576554
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: 55 (25.8 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