Alignments for a candidate for pimF in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Caulobacter crescentus NA1000

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate CCNA_03293 CCNA_03293 multifunctional fatty acid oxidation complex subunit alpha FadJ

Query= metacyc::MONOMER-20678
         (699 letters)



>FitnessBrowser__Caulo:CCNA_03293
          Length = 696

 Score =  746 bits (1927), Expect = 0.0
 Identities = 390/690 (56%), Positives = 495/690 (71%), Gaps = 6/690 (0%)

Query: 1   MSEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFI 60
           ++ V   + +  + +VT++SPPVNALSAAVR G+    +AA+AD AV+AIVL+C G+TFI
Sbjct: 8   INAVTDFSVEGDIGVVTLNSPPVNALSAAVREGLQGAFDAAIADAAVKAIVLICDGKTFI 67

Query: 61  AGADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAK 120
           AGADITEFGK    P+L DV   +ENSPKP IAAIHGTALGGGLEVAL  ++RVAV  AK
Sbjct: 68  AGADITEFGKAMTGPSLQDVQNVIENSPKPVIAAIHGTALGGGLEVALVANYRVAVPSAK 127

Query: 121 LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN--LV 178
            GLPEV +GLLPGAGGTQRLPR VG E A++M+  G  + A  A   GL +E+VE   L 
Sbjct: 128 AGLPEVNIGLLPGAGGTQRLPRIVGVEKALEMVTTGQHVPAKAAHAMGLFDELVEEGKLR 187

Query: 179 AGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADA 238
            GA+AFAK V+AE RPL+++RD + K+ AA+    IF     A  KK RG  AP      
Sbjct: 188 EGAIAFAKAVVAENRPLKKVRDLNEKVEAARGKPEIFEAFRKANAKKFRGFMAPENNIKC 247

Query: 239 IGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRV 298
           I AA++LPF+EGLK ER+ FM+L+   QS AQRY FFAER+AAK+  VPD T   PV +V
Sbjct: 248 IEAAVNLPFDEGLKAERKLFMELMTGSQSAAQRYVFFAERQAAKIPDVPDDTPTIPVKKV 307

Query: 299 AIIGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAK 358
            +IGAGTMGGGIAM+F NAGIPVT+IE  +E L+RG+GI++KN+E TA +G L  D   K
Sbjct: 308 GVIGAGTMGGGIAMNFLNAGIPVTIIEAKQENLERGVGIIRKNYENTAKKGRLTQDDVEK 367

Query: 359 RMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEI 418
           RMAL+T  + +E + D D+IIEAVFE M +KKEVFT +D  AKPGA+LA+NTSYL +D I
Sbjct: 368 RMALLTPSMEMEALADCDMIIEAVFELMEIKKEVFTKLDKIAKPGAILATNTSYLDVDAI 427

Query: 419 AATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDG 478
           AA T RP+ V+G HFFSPANVM+L E+VRG KT+ D + T + ++K I KVPV+VGVC G
Sbjct: 428 AAVTSRPESVIGTHFFSPANVMRLLELVRGDKTSKDVIATCMKLSKTIGKVPVLVGVCYG 487

Query: 479 FVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRG 538
           FVGNRMLA R ++++KL+ EGA+P  VD V+  FG+PMGPFAM DLAGLDIGW   K   
Sbjct: 488 FVGNRMLAQRQREAQKLILEGAMPWDVDRVLYDFGLPMGPFAMSDLAGLDIGWDPAKTS- 546

Query: 539 IKSEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDE 598
             S + + LCE  R GQK GKG+Y Y++ +R   P P VE +I D   K  ++RR+ITD+
Sbjct: 547 -SSTVREVLCEMDRRGQKNGKGFYDYDE-NRNAKPSPVVEEVIRDFAEKRQIQRREITDQ 604

Query: 599 EILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658
           EILER +YPM+NEGA+ILEE  A R SDID+VW+ GYGWP+Y GGPM + + VGL  +  
Sbjct: 605 EILERCLYPMVNEGAKILEEGKAIRASDIDIVWINGYGWPVYSGGPMFWGELVGLDKVLA 664

Query: 659 RLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           ++  +     D   +P+ LL RL AEGK F
Sbjct: 665 KMKQFHAELGD-DFKPSALLERLVAEGKGF 693


Lambda     K      H
   0.317    0.134    0.383 

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: 1175
Number of extensions: 61
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: 699
Length of database: 696
Length adjustment: 39
Effective length of query: 660
Effective length of database: 657
Effective search space:   433620
Effective search space used:   433620
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: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources