GapMind for catabolism of small carbon sources

 

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

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)

Query= SwissProt::O34521
         (452 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833
          Length = 571

 Score =  459 bits (1182), Expect = e-134
 Identities = 232/455 (50%), Positives = 309/455 (67%), Gaps = 11/455 (2%)

Query: 5   LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIGISK 64
           LQ+LG++ MLPIA+LP  G++L LG  D+ NI  ++ AG  +F +L +IFAIGIA+G ++
Sbjct: 9   LQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLAMIFAIGIAVGFAR 68

Query: 65  DSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGF 124
           D+NG AGL+G I YL++ +  K +D + NM +  GI++GL+AG  YNRFKD KLPEYL F
Sbjct: 69  DNNGTAGLAGVIGYLVMISTLKALDPSINMGMLAGIVSGLMAGALYNRFKDIKLPEYLAF 128

Query: 125 FSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIP 184
           F GRR VPI+T    + L  +FG +WPPIQ  INSFG  M+  G  GA +FGLFNRLLI 
Sbjct: 129 FGGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGINSFGTLMMESGSFGAFVFGLFNRLLIV 188

Query: 185 LGLHHVLNNIFWFQFGEYNG------VTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAAC 238
            GLHH+LNN+ WF FG +        VTGDL+R+FA DP  G +MTG FP+M+FGLPAAC
Sbjct: 189 TGLHHILNNMAWFVFGNFTDPTTGALVTGDLSRYFAGDPKGGQFMTGMFPMMIFGLPAAC 248

Query: 239 LAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFI 298
           LAM   A P++RK   G+ +  ALTAF+TG+TEPIEFAFMFL+PLL+ +HA+LTGLS+ I
Sbjct: 249 LAMYRNALPARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHALLTGLSMAI 308

Query: 299 VNWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPG 358
            N L I  GF+FS G ID +L +G +    L+  VG+ YA +Y++VF   I+  +LKTPG
Sbjct: 309 TNALNIHLGFTFSGGFIDMILGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIRRFDLKTPG 368

Query: 359 REDD-DVDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLK 417
           RE   DV++V       +      +K LGG ENL T+  C TRLRL + D     +  LK
Sbjct: 369 RETSADVEQVA---VADNERAGAYIKALGGAENLITVGACTTRLRLDMVDRNKASDTDLK 425

Query: 418 KAGAKGVVKSG-GQSVQVIIGPNVEFAAEELRAAV 451
             GA  VV+ G G S+QV++GP  +  A+E+R A+
Sbjct: 426 ALGAMAVVRPGKGGSLQVVVGPMADAIADEIRLAM 460



 Score = 34.7 bits (78), Expect = 8e-06
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 382 LKGLGGKENLQTIDHCA-TRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNV 440
           L  LGG +N+  +D  A TR+RL + D   + E  LK  G +GV +  G    ++IG   
Sbjct: 492 LNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDGGIWHLLIGDKA 551

Query: 441 EFAAEELRAAV 451
              ++ L   V
Sbjct: 552 PTLSDALEVLV 562


Lambda     K      H
   0.326    0.144    0.429 

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: 709
Number of extensions: 36
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 452
Length of database: 571
Length adjustment: 34
Effective length of query: 418
Effective length of database: 537
Effective search space:   224466
Effective search space used:   224466
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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