Alignments for a candidate for pimF in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Paraburkholderia bryophila 376MFSha3.1

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate H281DRAFT_00916 H281DRAFT_00916 short chain enoyl-CoA hydratase /3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__Burk376:H281DRAFT_00916
          Length = 694

 Score =  679 bits (1751), Expect = 0.0
 Identities = 359/693 (51%), Positives = 481/693 (69%), Gaps = 12/693 (1%)

Query: 5   VTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGAD 64
           V   T D VA++T+++PPVN L  + R GI+E +  A  D A++AIVL  AG+ F  GAD
Sbjct: 3   VDYTTHDGVAVITLNNPPVNGLGLSTRAGIVEGIERAQNDAAIKAIVLTGAGKAFSGGAD 62

Query: 65  ITEFGKPP--QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLG 122
           ITEF  P   Q P L  VI  +E SPKP +AAIH  A+GGGLE+ALG H+R+A   A++ 
Sbjct: 63  ITEFNTPKATQEPTLATVIKTVEGSPKPVVAAIHSVAMGGGLELALGAHYRIAAPGAQIA 122

Query: 123 LPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE-NLVAGA 181
           LPEVKLG+LPGAGGTQRLPRA+G E A+ MIV G+P+ + +  + GL +E+ + +L   A
Sbjct: 123 LPEVKLGILPGAGGTQRLPRAIGLEAALNMIVSGAPVMSQDLARSGLFDELADGDLTEAA 182

Query: 182 VAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGA 241
           +AFA+KV A++ P  ++R+   +   A+       N+VA +   A+   AP  C DA+ A
Sbjct: 183 LAFARKVGAKEGPHPKVRERKIEHPNAEGFIQFARNSVATV---AKNFPAPLKCIDAVEA 239

Query: 242 AIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAII 301
            +   F++GL  ERE F+ LV + +S+A R+AFF ER A+K+  VP  T  R + +VA+I
Sbjct: 240 GVKNGFDKGLAVERECFVALVQTPESRALRHAFFGERAASKIPDVPADTPVREIRQVAVI 299

Query: 302 GAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMA 361
           GAGTMGGGIAM+F +AGIPVTL+ET +E L RGL  ++KN+EAT  +G L P+A  +RMA
Sbjct: 300 GAGTMGGGIAMNFISAGIPVTLLETKQEALDRGLATIRKNYEATVKKGKLKPEALEERMA 359

Query: 362 LITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAAT 421
           LIT  +  +++K+ADLI+EAVFE + VK++VF  +D  AK GA+LASNTS L +D+IAA 
Sbjct: 360 LITPTLSYDDLKNADLIVEAVFEELGVKEQVFKRLDEVAKSGAILASNTSTLDVDKIAAF 419

Query: 422 TKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVG 481
           T+RPQDV+GMHFFSPANVMKL E+VRG +TA D L T + +AKKI K  VV GVCDGF+G
Sbjct: 420 TRRPQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMKLAKKIKKTAVVSGVCDGFIG 479

Query: 482 NRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK- 540
           NRM+    +Q+  +L EGALP QVD  + KFG  MGPF M DLAG DIGW  RK R  + 
Sbjct: 480 NRMIEQYIRQALFMLDEGALPAQVDRAIEKFGFAMGPFRMSDLAGNDIGWAIRKRRYEEH 539

Query: 541 -----SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDI 595
                S+IAD LCE GRFGQKTG G+Y Y+ G R   P   V+ +I     +   +RR I
Sbjct: 540 PEMHYSKIADRLCETGRFGQKTGGGWYDYKAGDRTAHPSKLVDDMIVAYSNETNTQRRKI 599

Query: 596 TDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKH 655
            D+EI+ER+V+ ++NEGA+ILEE IA++PSDID+V+L GYG+P+YRGGPM YAD+VGL +
Sbjct: 600 GDDEIVERLVFALVNEGAKILEEGIASKPSDIDMVYLTGYGFPLYRGGPMLYADTVGLYN 659

Query: 656 IAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           +   +  YA   N  + + AP +A LAA+G+ F
Sbjct: 660 VERAIRRYASQPNGDAWQLAPSIAELAAQGRGF 692


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: 1139
Number of extensions: 50
Number of successful extensions: 6
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: 694
Length adjustment: 39
Effective length of query: 660
Effective length of database: 655
Effective search space:   432300
Effective search space used:   432300
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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Protein sequences (fasta format)
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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