GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Caulobacter crescentus NA1000

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate CCNA_03243 CCNA_03243 NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Caulo:CCNA_03243
          Length = 499

 Score =  470 bits (1210), Expect = e-137
 Identities = 245/487 (50%), Positives = 336/487 (68%), Gaps = 4/487 (0%)

Query: 11  DKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVF 70
           ++   LA  ++  I+G+   AA   TF  V P     L  +   ++ D++RA++ AR  F
Sbjct: 12  ERLAKLAPPSQAVIDGDLVEAASGATFHNVSPRDGQVLNLVTACQADDVERAVAGARAAF 71

Query: 71  ERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRW 130
           E G W    P ++KAVL +LA+LME  A+ELALLE+LD GKPI  +   DIP A    RW
Sbjct: 72  EDGRWRDQGPRQKKAVLFRLAELMERDADELALLESLDVGKPISDARNVDIPLAINTCRW 131

Query: 131 YAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVIL 190
           YAEA+DKVYGEV T+ +  L+  V EP+GVI AIVPWNFPL +  WK+ PALA GNSV+L
Sbjct: 132 YAEALDKVYGEVGTSPADRLSYAVHEPLGVIGAIVPWNFPLHMAMWKVAPALAMGNSVVL 191

Query: 191 KPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGK 250
           KP+E+SPL+A++L  LA EAGLP GVLNV+ G G  AG+AL+   D+D IAFTGS   G+
Sbjct: 192 KPAEQSPLTALKLGALALEAGLPPGVLNVIPGLGGVAGEALALSMDVDMIAFTGSGPVGR 251

Query: 251 QLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLL 310
           +L++ +  SN+KRV LE GGKS  IVFADCPDL+ AA A A G+FYNQG+VC A +RLL+
Sbjct: 252 RLMEYSARSNLKRVSLELGGKSPQIVFADCPDLEAAAQAAAWGVFYNQGEVCTAASRLLV 311

Query: 311 EESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLD 369
           E  I D FLA + + A+  + G PLDP+T  G ++     ++   +I   +S+G + +L 
Sbjct: 312 EAPIKDAFLARVIEVAKGMKVGDPLDPSTQFGAMVSERQMNTALDYIATADSQGARRVLG 371

Query: 370 GRNAGLAAA---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLG 426
           G+     A    + PTIF  V P+ +L+REE+FGPVL V  F+SE++A++LAND+ YGL 
Sbjct: 372 GQRVRQEAGGFYVEPTIFDQVRPDQTLAREEVFGPVLGVMTFSSEDEAMRLANDTVYGLA 431

Query: 427 AAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTEL 486
           A +WT D+S+A R +RRLKAG V+VN ++  D+T+PFGG+KQSG GRD+SLHAL K+ +L
Sbjct: 432 AGLWTADVSKALRGARRLKAGLVWVNGWDACDITMPFGGFKQSGFGRDRSLHALHKYADL 491

Query: 487 KTIWISL 493
           K++ ++L
Sbjct: 492 KSVSVTL 498


Lambda     K      H
   0.317    0.133    0.389 

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: 603
Number of extensions: 22
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: 495
Length of database: 499
Length adjustment: 34
Effective length of query: 461
Effective length of database: 465
Effective search space:   214365
Effective search space used:   214365
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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