GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03230
          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 (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