Alignments for a candidate for acn in Lacinutrix algicola AKS293

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Lacinutrix algicola AKS293

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_055435324.1 ASC41_RS03870 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= reanno::Dino:3608667
         (930 letters)



>NCBI__GCF_001418085.1:WP_055435324.1
          Length = 924

 Score = 1370 bits (3545), Expect = 0.0
 Identities = 692/920 (75%), Positives = 792/920 (86%), Gaps = 6/920 (0%)

Query: 1   MSLYTAYLEEIAARKEQGLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPGT 60
           M++Y  YL++I  RKEQGL P+PID A L S+II QIKD  +EHR +SL FFIYN LPGT
Sbjct: 1   MNIYNDYLKQIENRKEQGLHPQPIDGAELLSQIIEQIKDLDNEHREESLNFFIYNVLPGT 60

Query: 61  TSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQA 120
           TSAA  KA+FLKEIILGES+V EITP FA E LSHM+GGPSV+VLLDIALG+DA LA Q+
Sbjct: 61  TSAATVKAKFLKEIILGESIVKEITPTFALEQLSHMKGGPSVKVLLDIALGNDADLAKQS 120

Query: 121 AEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIAA 180
           AE+LKTQVFLYEADTDRL+ A ++G+ +A  I++SYA+AEFFT LPEI+++IEVVTYIA 
Sbjct: 121 AEILKTQVFLYEADTDRLEEAFKSGSEIAKDIIESYAKAEFFTKLPEIDEKIEVVTYIAG 180

Query: 181 EGDISTDLLSPGNQAHSRSDRELHGKCMI--SEAAQKEIEALKLQHPGKRVMLIAEKGTM 238
            GDISTDLLSPG  AHSRSDRELHG+CM   ++  Q E+ ALK QHP KRVMLIAEKGTM
Sbjct: 181 VGDISTDLLSPGGDAHSRSDRELHGQCMFEHNKDMQNELLALKEQHPDKRVMLIAEKGTM 240

Query: 239 GVGSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKN 298
           GVGSSRMSGVNNVALWTG   S YVPF+N APV+AGTNGI+PIF+TTVGVTGGIG+DLKN
Sbjct: 241 GVGSSRMSGVNNVALWTGVPFSKYVPFINFAPVIAGTNGIAPIFLTTVGVTGGIGLDLKN 300

Query: 299 WVKKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSP 358
           WV++ D +GN + + DG PIL++ YSV TGT+L I+TK +KL + D  +EL D+S+AF+P
Sbjct: 301 WVQQKDAEGNTVRDEDGEPILKETYSVATGTILTINTKEKKLYNGD--KELKDISAAFTP 358

Query: 359 QAVEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANA 418
           Q +EFMKAGGSYAVVFGKKLQT AA+ LG+E   V+A AKE+S EGQGLTAVEKIFN NA
Sbjct: 359 QKMEFMKAGGSYAVVFGKKLQTFAAKALGIEAPQVYATAKEVSIEGQGLTAVEKIFNKNA 418

Query: 419 RGVTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTAS 478
            G T G  LHAGS VR +VNIVGSQDTTGLMTSQELE MAATV+SP VDGAYQSGCHTAS
Sbjct: 419 VG-TSGATLHAGSYVRAEVNIVGSQDTTGLMTSQELEMMAATVISPIVDGAYQSGCHTAS 477

Query: 479 VWDLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSH 538
           VWD K++AN PRLM+FM+ FGLIT RDPKG Y  MTDVIHKVLNDITV DWDIIIGGDSH
Sbjct: 478 VWDDKSKANIPRLMSFMNDFGLITGRDPKGKYFPMTDVIHKVLNDITVGDWDIIIGGDSH 537

Query: 539 TRMSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLA 598
           TRMSKGVAFGADSGTVALALATGEA+MPIPESVKVTFKG+M  +MDFRDVVHATQ QML 
Sbjct: 538 TRMSKGVAFGADSGTVALALATGEASMPIPESVKVTFKGQMKSYMDFRDVVHATQQQMLK 597

Query: 599 QHG-DNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRI 657
           Q G +NVFQGRVIEVHIGTL AD+AFTFTDWTAEMKAKASICIS DDTLIESLEIAK RI
Sbjct: 598 QFGGENVFQGRVIEVHIGTLTADEAFTFTDWTAEMKAKASICISEDDTLIESLEIAKGRI 657

Query: 658 QVMIDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPM 717
           Q+MI+KGMDN  Q+L GL+ KA  RI E+++G KP+L+PD  A+Y AEV++DLDQIVEPM
Sbjct: 658 QIMIEKGMDNAKQVLKGLVDKAETRIIELKTGMKPSLRPDANAKYHAEVIIDLDQIVEPM 717

Query: 718 IADPDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKA 777
           IADPDV+N DVSKRYTHD IRP+SYYG  KK+DLGFVGSCMVHKGD+KI+AQML+N+E  
Sbjct: 718 IADPDVNNEDVSKRYTHDNIRPLSYYGGTKKVDLGFVGSCMVHKGDMKILAQMLKNVEAQ 777

Query: 778 NGEVKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLE 837
            G+V+FKAPL++A PTYNI+DELK EGDW+VL +Y+GFEFDD+APK +ART YEN+LYLE
Sbjct: 778 YGKVEFKAPLIVAPPTYNIVDELKAEGDWEVLVRYSGFEFDDNAPKGEARTGYENMLYLE 837

Query: 838 RPGCNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRT 897
           RPGCNLCMGNQEKAA GDTV+ATSTRLFQGRVV DS  KKGESLL STPVVVLS ILGRT
Sbjct: 838 RPGCNLCMGNQEKAAPGDTVMATSTRLFQGRVVKDSGEKKGESLLSSTPVVVLSTILGRT 897

Query: 898 PTVEEYKTAVEGINLTKFAP 917
           PT+EEY+ AV+GI LTKF P
Sbjct: 898 PTMEEYEAAVDGIVLTKFKP 917


Lambda     K      H
   0.316    0.132    0.374 

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: 2282
Number of extensions: 88
Number of successful extensions: 5
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: 930
Length of database: 924
Length adjustment: 43
Effective length of query: 887
Effective length of database: 881
Effective search space:   781447
Effective search space used:   781447
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 (21.6 bits)
S2: 57 (26.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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