GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuA in Shewanella loihica PV-4

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 5211138 Shew_3554 glutamine synthetase (RefSeq)

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



>FitnessBrowser__PV4:5211138
          Length = 469

 Score =  140 bits (352), Expect = 1e-37
 Identities = 133/423 (31%), Positives = 185/423 (43%), Gaps = 51/423 (12%)

Query: 54  VTGDYPEDGTL---------TGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGT 104
           V  D+ EDG +          G+ + DMV +PD +T  + P+  + TA +  D +   GT
Sbjct: 39  VDADFFEDGKMFDGSSIAGWKGINESDMVLMPDPTTFVLDPFTEETTALIRCDILE-PGT 97

Query: 105 PVAIS--PRRVLRRVLELYKAKGWKP--VIAPELEFYLVDMNK-DPDLP----------- 148
                  PR + ++  E   + G     +I PE EF+L D  K   D+            
Sbjct: 98  MTGYDRDPRSIAKKAEEYMVSTGIADTVLIGPEPEFFLFDDVKFGTDMSGCFVKLDAKEA 157

Query: 149 -----LQPPIGRTG-RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVGAA 202
                     G TG RP      + +  V+    L   +    E     V+   HEV  A
Sbjct: 158 AWNSGTHYEDGNTGHRPFVKGGYFPVAPVDSSQDLRSAMCLVLEEMGQVVEAHHHEVATA 217

Query: 203 -QMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVD 261
            Q EI        + AD + + K  V   A  +   ATFM KP+ G+ GS MH+HQSL  
Sbjct: 218 GQNEIATRFNKLTEKADEIQILKYVVHNMAHAYGKTATFMPKPIVGDNGSGMHVHQSLAK 277

Query: 262 EETGHNLFTGPDG---KPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINV 318
           +  G NLF+G        T+L+  YI G+ K+  AL     P  NSY+RL     AP+ +
Sbjct: 278 D--GVNLFSGDKYAGLSETALY--YIGGIIKHARALNAFTNPSTNSYKRLVPHFEAPVML 333

Query: 319 AWGYDNRTVGFRIPH-SGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPL 377
           A+   NR+   RIP    P ARRIE R P    NPYLA AA L AG  G+  K+   E +
Sbjct: 334 AYSARNRSASIRIPVVPSPKARRIETRFPDPTANPYLAFAALLMAGLDGIQNKIHPGEAM 393

Query: 378 LSDGYELPY-------QLPRNLEEGLTLMGACEPI---AEVLGEKFVKAYLALKETEYEA 427
             D Y+LP        Q+  +LE  L  + A         V  + F+ +Y+ALK  E E 
Sbjct: 394 DKDLYDLPAEEAAEIPQVATSLENALENLDADREFLTKGGVFSDDFIDSYIALKTAEAEK 453

Query: 428 FFR 430
             R
Sbjct: 454 VAR 456


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: 526
Number of extensions: 33
Number of successful extensions: 4
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: 469
Length adjustment: 33
Effective length of query: 411
Effective length of database: 436
Effective search space:   179196
Effective search space used:   179196
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.

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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