Alignments for a candidate for acn in Amphritea japonica JAMM 1866

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Amphritea japonica JAMM 1866

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_019622309.1 G329_RS0112385 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

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



>NCBI__GCF_000381785.1:WP_019622309.1
          Length = 931

 Score = 1344 bits (3478), Expect = 0.0
 Identities = 688/920 (74%), Positives = 780/920 (84%), Gaps = 7/920 (0%)

Query: 1   MSLYTAYLEEIAARKEQ-GLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPG 59
           MS Y+ YLEEI  RK+  GL PKPID A L SEIIAQIKD  +EHR  SL FFIYN LPG
Sbjct: 1   MSYYSDYLEEIEVRKKDLGLNPKPIDSAELLSEIIAQIKDVGNEHREASLNFFIYNILPG 60

Query: 60  TTSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQ 119
           TT AAG KA FLK+I LG+  VAEI+ +FA E LSHM+GGPSVE LLDIAL DDA  AA 
Sbjct: 61  TTPAAGVKATFLKDIALGKETVAEISAEFALEQLSHMKGGPSVEALLDIALSDDAQAAA- 119

Query: 120 AAEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIA 179
           AAEVLK+QVFLY+AD+ RL  A +AGNA+A  IL+SY++AEFFT L +I + I+V+TYIA
Sbjct: 120 AAEVLKSQVFLYDADSARLADAFKAGNAIAKDILESYSKAEFFTKLSDIPETIKVITYIA 179

Query: 180 AEGDISTDLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPGKRVMLIAEKGTMG 239
            EGDISTDLLSPGNQ+HSR+DRELHGKCMIS  AQ+EI  +  Q+P  +VMLIAEKGTMG
Sbjct: 180 GEGDISTDLLSPGNQSHSRADRELHGKCMISPEAQQEIAEMGKQNPDAKVMLIAEKGTMG 239

Query: 240 VGSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKNW 299
           VGSSRMSGVNNVALW G++ SPY+PF+N  PVVAGTNGI+PIF+TTVGVTGGIG+DLKNW
Sbjct: 240 VGSSRMSGVNNVALWAGEKTSPYIPFINNNPVVAGTNGIAPIFLTTVGVTGGIGLDLKNW 299

Query: 300 VKKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSPQ 359
           VKK D +G  + + +G+P+LE+ YSV TGTVL IDTKA+KL + D  +EL D++ AF+PQ
Sbjct: 300 VKKTDANGEVVRDANGDPVLEEAYSVATGTVLTIDTKAKKLYNGD--QELVDIADAFTPQ 357

Query: 360 AVEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANAR 419
            VEFMKAGGSYAV FGKKLQT AAETLGVE   V+A +KEISHEGQGLTAVEKIFN NA 
Sbjct: 358 KVEFMKAGGSYAVTFGKKLQTFAAETLGVEAPAVYAQSKEISHEGQGLTAVEKIFNRNAV 417

Query: 420 GVTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTASV 479
           GVT    LH GSDVRV+VNIVGSQDTTG MT QELEAMAA+ +S +VDGA+QSGCHTASV
Sbjct: 418 GVTSKTPLHTGSDVRVKVNIVGSQDTTGPMTCQELEAMAASTISTSVDGAFQSGCHTASV 477

Query: 480 WDLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSHT 539
           WD KA+ANTP+LMAFM+ FG ITARDPK VYHSMTDVIHKVLNDITV D  IIIGGDSHT
Sbjct: 478 WDNKAKANTPKLMAFMNAFGAITARDPKHVYHSMTDVIHKVLNDITVDDRAIIIGGDSHT 537

Query: 540 RMSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLAQ 599
           RMSKGVAFGADSGTVA+ALATGE+ MPIPESVKVTFKG M  HMDFRD+VHATQAQML +
Sbjct: 538 RMSKGVAFGADSGTVAIALATGESAMPIPESVKVTFKGSMKPHMDFRDIVHATQAQMLKK 597

Query: 600 H-GDNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRIQ 658
             G+NVFQGRVIEV IGTLLADQAFTFTDWTAEMKAKASICIS DDTLI+SLE+AK RIQ
Sbjct: 598 FGGENVFQGRVIEVQIGTLLADQAFTFTDWTAEMKAKASICISTDDTLIQSLELAKSRIQ 657

Query: 659 VMIDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPMI 718
           +MI+KGM+N+  ML GLI  A+ RIAE++SGE PAL PDD A+Y+AE+VVDLD I EPMI
Sbjct: 658 IMINKGMENEAGMLQGLIDLADKRIAEVKSGEAPALAPDDNAKYYAELVVDLDVIEEPMI 717

Query: 719 ADPDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKAN 778
           ADPDV+N DVSKRYTHD IRP SYY   +K+DLGFVGSCMVHKGD++I+A MLRNLEK  
Sbjct: 718 ADPDVNNEDVSKRYTHDVIRPASYYDG-RKVDLGFVGSCMVHKGDMQIIAAMLRNLEK-K 775

Query: 779 GEVKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLER 838
           G + FKAPLV+A PTYNI+DELK EGDW++L+K+AGFEF D  PKE ART+YENILYLER
Sbjct: 776 GPITFKAPLVVAPPTYNIVDELKAEGDWELLEKFAGFEFSDENPKEAARTKYENILYLER 835

Query: 839 PGCNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRTP 898
           PGCNLCMGNQEKA  GDTVLATSTRLFQGRVV D+  KKGESLLGSTP+VVLS +LGR P
Sbjct: 836 PGCNLCMGNQEKAEAGDTVLATSTRLFQGRVVEDTAEKKGESLLGSTPMVVLSCVLGRFP 895

Query: 899 TVEEYKTAVEGINLTKFAPP 918
           T+EEYK AVEGI+LT FAPP
Sbjct: 896 TLEEYKEAVEGIDLTTFAPP 915


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: 2232
Number of extensions: 92
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: 930
Length of database: 931
Length adjustment: 43
Effective length of query: 887
Effective length of database: 888
Effective search space:   787656
Effective search space used:   787656
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