Alignments for a candidate for pimF in Tistlia consotensis USBA 355

GapMind for catabolism of small carbon sources

Alignments for a candidate for pimF in Tistlia consotensis USBA 355

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate WP_085121628.1 B9O00_RS06390 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

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



>NCBI__GCF_900177295.1:WP_085121628.1
          Length = 707

 Score =  811 bits (2095), Expect = 0.0
 Identities = 425/699 (60%), Positives = 517/699 (73%), Gaps = 1/699 (0%)

Query: 2   SEVVTRATQDQVAIVTVDSPPVNALSAAVRRGILENVNAAVADPAVQAIVLVCAGRTFIA 61
           ++ V  +T   VA+VT+ +PPVNAL  AVR GI+  +  A ADPAV+A+VL  AGRTF  
Sbjct: 9   NDAVGYSTDGDVAVVTIANPPVNALGYAVRSGIVAALERAAADPAVKAVVLTGAGRTFSG 68

Query: 62  GADITEFGKPPQPPALNDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVKEAKL 121
           GADITEFGKPP+ P L+ VI   E+  KP +AAI G ALGGGLE+AL CH RVA  +A+L
Sbjct: 69  GADITEFGKPPREPGLSAVIRHCESLAKPVVAAIRGVALGGGLELALACHARVAAPDARL 128

Query: 122 GLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVEN-LVAG 180
           GLPEVKLGLLPGAGGTQRLPR VGPE AV+MIV G+PI AA+A   GLV+ +VE+ LVAG
Sbjct: 129 GLPEVKLGLLPGAGGTQRLPRVVGPEAAVEMIVTGTPIAAAKAATLGLVDGIVEDDLVAG 188

Query: 181 AVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMTKKARGLEAPFACADAIG 240
           A A A+ ++  ++    +RD + +LAA + D S F      +T++ RGLEAP AC  A+ 
Sbjct: 189 ATAHARALVESRQTPVPVRDREDRLAATRRDPSAFEAKAKQLTQRTRGLEAPLACVRAVR 248

Query: 241 AAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPRPVSRVAI 300
            A+D PF+E L +ER  F +L+   QSKAQR+ FFAEREA KV GV     PRPV+RV +
Sbjct: 249 MALDTPFDEALSRERALFTELLDGFQSKAQRHLFFAEREATKVAGVGREVTPRPVARVGV 308

Query: 301 IGAGTMGGGIAMSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLPPDAPAKRM 360
           +GAGTMGGGIAM+FANAGIPVTL+E   E L+RGLG+++KN++ + ARG L      +R+
Sbjct: 309 VGAGTMGGGIAMTFANAGIPVTLVEMNREALERGLGVIRKNYDLSVARGSLGEQERDRRL 368

Query: 361 ALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSYLSIDEIAA 420
           ALITG    E++  ADL+IEAVFE MAVKKEVF  +D  A+PGA+LASNTSYL ID IA 
Sbjct: 369 ALITGSTRYEDLAVADLVIEAVFEEMAVKKEVFGRLDRIARPGAILASNTSYLDIDAIAD 428

Query: 421 TTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVVVGVCDGFV 480
            T RP DV+G HFFSPANVMKL EIVRG +TAPD L T + +AK+I KVPVVVGVC GFV
Sbjct: 429 ATGRPADVVGTHFFSPANVMKLLEIVRGRRTAPDVLATLLGLAKRIGKVPVVVGVCHGFV 488

Query: 481 GNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIGWRSRKDRGIK 540
           GNRMLAARS ++E LL EGALPQ+VD   T FG PMGPFAMGDLAGLD+GWR+RK  G  
Sbjct: 489 GNRMLAARSAENEALLLEGALPQEVDRAFTDFGFPMGPFAMGDLAGLDVGWRNRKSLGRT 548

Query: 541 SEIADALCEAGRFGQKTGKGYYKYEQGSRAPMPDPEVETLINDTLAKLGLKRRDITDEEI 600
           + IADALCEAGRFGQKTG+G+Y+YE GSR P PDP VE LI     + G++RR I  EEI
Sbjct: 549 AVIADALCEAGRFGQKTGEGFYRYEAGSRRPEPDPWVEALIAGKARERGIERRPIAAEEI 608

Query: 601 LERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIYRGGPMHYADSVGLKHIAERL 660
           +ER +YPMINEGARILEE IAARPSDIDV W+ GYG+P+ +GGPM +AD VGL  I ERL
Sbjct: 609 VERTLYPMINEGARILEEGIAARPSDIDVAWVDGYGFPVGKGGPMFWADHVGLATIVERL 668

Query: 661 SAYAKATNDPSLEPAPLLARLAAEGKTFASLTQPSKAAA 699
             +   T       APLL RLAA+G +FA+L + + A A
Sbjct: 669 DDWHGKTGRELFAAAPLLRRLAADGGSFAALGRKAGAGA 707


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: 1355
Number of extensions: 65
Number of successful extensions: 2
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: 707
Length adjustment: 39
Effective length of query: 660
Effective length of database: 668
Effective search space:   440880
Effective search space used:   440880
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
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Rules (tab-delimited)
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 2024 update 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