GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Sinorhizobium meliloti 1021

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate SMc00762 SMc00762 glutamine synthetase

Query= reanno::BFirm:BPHYT_RS23160
         (444 letters)



>FitnessBrowser__Smeli:SMc00762
          Length = 478

 Score =  511 bits (1316), Expect = e-149
 Identities = 247/444 (55%), Positives = 318/444 (71%), Gaps = 8/444 (1%)

Query: 6   DFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLT 65
           D+LK   + +IE I PD+AG+ARGK++P SKF S  S+ LP A+   T++G+YPE+   T
Sbjct: 38  DWLKIRGIEDIECITPDLAGVARGKMMPTSKFTSNTSLALPSAIYRHTISGEYPEE---T 94

Query: 66  GV-----TDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLEL 120
           G       D D+  VPD ST+ ++PW  DPTAQVI D V   G  ++ +PR VL+RV+EL
Sbjct: 95  GQFRYDSRDSDIKLVPDLSTLSIVPWESDPTAQVICDIVGSQGEQISYTPRNVLKRVIEL 154

Query: 121 YKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFED 180
           Y+ KGWKPV+APE+EFYLV  N DPD PL+PP GR+GR   G Q YSI  +NEFD L +D
Sbjct: 155 YRQKGWKPVVAPEIEFYLVAQNDDPDYPLRPPKGRSGRSILGGQGYSIAGINEFDELIDD 214

Query: 181 IYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATF 240
           IY + E Q LE+DTLIHE G AQ+EIN  HGDP++LAD VFLFKRT+REAAL+H +YATF
Sbjct: 215 IYHFSEKQGLEIDTLIHEEGPAQLEINLRHGDPIELADQVFLFKRTIREAALKHGIYATF 274

Query: 241 MAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAP 300
           MAKPM+G+PGSAMH+HQS++D ETG N+F+ PDG P+  F S+I G+Q Y P  + + AP
Sbjct: 275 MAKPMQGQPGSAMHIHQSVIDIETGRNIFSNPDGSPSQAFFSFIGGMQLYVPRTLSMMAP 334

Query: 301 YINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATL 360
           Y+NSYRRL+  M+AP+N AWGYDNRT  FRIP S P ARRIENR+P  D NPYLA+AA+L
Sbjct: 335 YVNSYRRLTPDMSAPVNTAWGYDNRTTAFRIPVSDPVARRIENRLPSSDANPYLALAASL 394

Query: 361 AAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLAL 420
             GYLG+ + L+AT P      E   +LPR L E ++L+ +   +AEV   +F+  Y  +
Sbjct: 395 GCGYLGIIEGLQATPPTEHTANEGEIELPRGLLEAVSLLESAPALAEVFSAEFIAIYAGV 454

Query: 421 KETEYEAFFRVISSWERRHLLLHV 444
           K  E+E F +VIS WER  LLL+V
Sbjct: 455 KRGEFETFMQVISPWEREFLLLNV 478


Lambda     K      H
   0.321    0.138    0.418 

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: 669
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: 444
Length of database: 478
Length adjustment: 33
Effective length of query: 411
Effective length of database: 445
Effective search space:   182895
Effective search space used:   182895
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 (21.8 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