GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuA in Caulobacter crescentus NA1000

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate CCNA_03230 CCNA_03230 glutamine synthetase

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



>lcl|FitnessBrowser__Caulo:CCNA_03230 CCNA_03230 glutamine
           synthetase
          Length = 465

 Score =  551 bits (1421), Expect = e-161
 Identities = 268/446 (60%), Positives = 329/446 (73%), Gaps = 3/446 (0%)

Query: 1   MHDIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPE 60
           + +  D+  +  + EIE ++PD+AG+ARGKI+P  KF    SM LP AV  QT+TGD+PE
Sbjct: 21  IEEAKDWFARQHIEEIECVVPDLAGVARGKIMPVRKFLGSPSMNLPLAVFYQTITGDFPE 80

Query: 61  -DGTLTGV-TDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVL 118
            +G +  V +D D+   PD +T+  +PWA DPTAQVIHD  H DG PV  +PR+VLRRVL
Sbjct: 81  FEGAVNAVQSDTDIFLTPDFATLAAVPWAQDPTAQVIHDAFHPDGRPVEEAPRQVLRRVL 140

Query: 119 ELYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLF 178
            LY  KGW P++APE+EFYLVD N DPD PL+PPIGR+GRPETGRQ YSI AVNEFD LF
Sbjct: 141 ALYADKGWHPIVAPEIEFYLVDRNTDPDYPLKPPIGRSGRPETGRQGYSISAVNEFDALF 200

Query: 179 EDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYA 238
           ED+YEY E Q LE+DTLIHE G AQMEIN  HG PL+LAD VF+ KRT+REAAL H++YA
Sbjct: 201 EDMYEYSERQGLEIDTLIHESGVAQMEINLQHGHPLELADQVFMMKRTIREAALEHEIYA 260

Query: 239 TFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIF 298
           TFMAKPM  EPGSAMH+HQS+VD++ G NLF+  DG  +++F  +IAG Q Y PA+M I 
Sbjct: 261 TFMAKPMANEPGSAMHIHQSIVDKK-GRNLFSDEDGAESAMFHGFIAGQQTYLPAIMAIL 319

Query: 299 APYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAA 358
           APY+NSYRR+SR   AP+N  WGYDNRT G R+P SGP  RR+ENRIP  D NPYLAIAA
Sbjct: 320 APYVNSYRRISRDSGAPVNTQWGYDNRTCGLRVPPSGPNNRRVENRIPSSDANPYLAIAA 379

Query: 359 TLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYL 418
           +LAAGYLGM Q L+ +EP+  D      +LPR+L + L L  AC+P+ E+LG  F  AY 
Sbjct: 380 SLAAGYLGMVQGLKPSEPVSIDAGARGIELPRSLSDSLRLFVACQPLVEILGPTFCAAYD 439

Query: 419 ALKETEYEAFFRVISSWERRHLLLHV 444
            +K+ EYE F R IS WER  LLL+V
Sbjct: 440 RVKQAEYETFMRTISPWEREFLLLNV 465


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: 674
Number of extensions: 20
Number of successful extensions: 3
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: 465
Length adjustment: 33
Effective length of query: 411
Effective length of database: 432
Effective search space:   177552
Effective search space used:   177552
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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