GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pimF in Burkholderia phytofirmans PsJN

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate BPHYT_RS09560 BPHYT_RS09560 3-hydroxyacyl-CoA dehydrogenase

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



>FitnessBrowser__BFirm:BPHYT_RS09560
          Length = 694

 Score =  681 bits (1758), Expect = 0.0
 Identities = 363/693 (52%), Positives = 476/693 (68%), Gaps = 12/693 (1%)

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

Query: 65  ITEFGKPP--QPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLG 122
           ITEF  P   Q P L  VI  +E S KP IAAIH  A+GGGLE+ALG H+R+A   A++ 
Sbjct: 63  ITEFNTPKAGQEPTLATVIKIVEGSAKPVIAAIHSVAMGGGLELALGAHYRIAAPGAQIA 122

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

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

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

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

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

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

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

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

Query: 596 TDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKH 655
           +DEEI+ER+V+ ++NEGA+ILEE IA++ SDID+V+L GYG+P+YRGGPM YAD+VGL +
Sbjct: 600 SDEEIVERLVFALVNEGAKILEEGIASKASDIDMVYLTGYGFPLYRGGPMLYADTVGLYN 659

Query: 656 IAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
           +   +  YA   N  + + AP +A LAA+ + F
Sbjct: 660 VERAIRRYAARPNGDAWQLAPSIAELAAKNRGF 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: 1123
Number of extensions: 52
Number of successful extensions: 7
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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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