GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__BFirm:BPHYT_RS09560 BPHYT_RS09560
           3-hydroxyacyl-CoA dehydrogenase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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