Alignments for a candidate for pimF in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Acidovorax sp. GW101-3H11

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate Ac3H11_2523 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_2523
          Length = 699

 Score =  657 bits (1696), Expect = 0.0
 Identities = 359/692 (51%), Positives = 464/692 (67%), Gaps = 20/692 (2%)

Query: 13  VAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIAGADITEFG--K 70
           VA++T+ +PPVN L  A R+GI++ +  A AD AV++IV+  AG  F  GADI EFG  K
Sbjct: 11  VAVITMANPPVNGLGLATRQGIVDGLGRANADAAVKSIVITGAGGAFSGGADIKEFGTDK 70

Query: 71  PPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKLGLPEVKLGL 130
             Q P L  VIAA+ENS KP +AA+H  A+GGGLE+ALGCH+R+A     + LPEVKLGL
Sbjct: 71  SLQEPNLLSVIAAIENSAKPVVAAMHSVAMGGGLELALGCHYRIAAPGCSIALPEVKLGL 130

Query: 131 LPGAGGTQRLPRAVGPELAVQMIVGGSP-----IGAAEALK-HGLVEEVVENLVAGAVAF 184
           +PGAGGTQRLPR +G E A+ +IV G P     IGA    K    +    E+L A A+AF
Sbjct: 131 IPGAGGTQRLPRVIGVEAALNLIVSGEPVKSEMIGAVPGQKLFDKMAASAESLAAEALAF 190

Query: 185 AKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIGAAID 244
           A+ V A+ RPL  +R+   K +   A      N V  M   A+   AP  C DA+ AA  
Sbjct: 191 AQSV-ADARPLPLVRNFPCKHSEGDAYFQFARNMVKGM---AKNFPAPAKCVDAVEAATK 246

Query: 245 LPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAIIGAG 304
             F EG+  ERE F+ L+ + +S+A R+ F AER A+K+  V   T  R +  V +IGAG
Sbjct: 247 KKFAEGMLVEREIFINLMWTPESRALRHLFMAERAASKIPDVASDTPKRDIKLVGVIGAG 306

Query: 305 TMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRMALIT 364
           TMGGGI+M+F NAGIPV ++E  +E L RG+  ++KN+EA   +G L  D   +RMAL++
Sbjct: 307 TMGGGISMNFLNAGIPVKILEMKQEALDRGVATIKKNYEAQVKKGKLKQDKYDQRMALLS 366

Query: 365 GLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAATTKR 424
             +  ++ KD DLIIEAVFE M VK+ VF  +DA AKPGA+LASNTS L +D+IAA TKR
Sbjct: 367 TTLSYDDFKDCDLIIEAVFEEMGVKEAVFKQLDAVAKPGAILASNTSTLDVDKIAAFTKR 426

Query: 425 PQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFVGNRM 484
           PQDV+GMHFFSPANVMKL E+VRG +TA D L T ++I KKI K  VV GVCDGF+GNRM
Sbjct: 427 PQDVVGMHFFSPANVMKLLEVVRGKETAKDVLATVMAIGKKIKKTSVVSGVCDGFIGNRM 486

Query: 485 LAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK---- 540
           +   S+Q+  LL EG  PQQVD  V KFG  MGPF MGDLAG DIGW  RK R ++    
Sbjct: 487 IEQYSRQAGFLLDEGCTPQQVDKAVEKFGFAMGPFRMGDLAGNDIGWAIRKRRSVERADM 546

Query: 541 --SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDE 598
             S  AD LCE GRFGQKTG G+Y Y+ G R  +P   V  +I D   +LG+  R I+DE
Sbjct: 547 KYSRTADKLCELGRFGQKTGAGWYDYQAGKRDAIPSDLVNKMIEDHRKELGITPRKISDE 606

Query: 599 EILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAE 658
           EI++R+V+ ++NEGA ILE+ IA++  DID+V+L GYG+PI+RGGPMHYA  VGL ++ +
Sbjct: 607 EIVQRLVFALVNEGAHILEDGIASKSGDIDMVYLTGYGFPIHRGGPMHYASEVGLFNVVQ 666

Query: 659 RLSAYAKATNDPSL--EPAPLLARLAAEGKTF 688
            +  +A+   D +   +PAPLLA+LAAEGK F
Sbjct: 667 AMDRFARNPLDDAAFWKPAPLLAKLAAEGKAF 698


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: 1049
Number of extensions: 52
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: 699
Length adjustment: 39
Effective length of query: 660
Effective length of database: 660
Effective search space:   435600
Effective search space used:   435600
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