GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Oleispira antarctica RB-8

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_046009357.1 OLEAN_RS11565 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

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



>NCBI__GCF_000967895.1:WP_046009357.1
          Length = 928

 Score = 1356 bits (3509), Expect = 0.0
 Identities = 698/933 (74%), Positives = 785/933 (84%), Gaps = 10/933 (1%)

Query: 1   MSLYTAYLEEIAARKEQ-GLQPKPIDDAALTSEIIAQIKDPAHEHRADSLQFFIYNTLPG 59
           MSLYT YLEEI  RK   GL PKPID A L SEIIAQIKD  +  R  SL FFIYNT+PG
Sbjct: 1   MSLYTEYLEEIEVRKNDLGLNPKPIDTADLLSEIIAQIKDTGNAAREASLDFFIYNTIPG 60

Query: 60  TTSAAGAKAQFLKEIILGESVVAEITPDFAFELLSHMRGGPSVEVLLDIALGDDASLAAQ 119
           TTSAA  KA FLK+I LG   VAEITP+FA E LSHM+GGPSVE LLDIAL DDA   A 
Sbjct: 61  TTSAAVVKAAFLKDIALGTETVAEITPEFALEQLSHMKGGPSVEALLDIALSDDAQAKA- 119

Query: 120 AAEVLKTQVFLYEADTDRLKAAHEAGNAVATGILQSYARAEFFTTLPEIEDEIEVVTYIA 179
           A EVLK+QVFLYEADT R+  A +AGNA+A  +L+SYA AEFFT LPEI  +I+VVTYIA
Sbjct: 120 AGEVLKSQVFLYEADTSRIADAFKAGNAIAKDLLESYAAAEFFTKLPEIPAKIDVVTYIA 179

Query: 180 AEGDISTDLLSPGNQAHSRSDRELHGKCMISEAAQKEIEALKLQHPGKRVMLIAEKGTMG 239
           AEGDISTDLLSPGNQ+HSR+DRELHG+CMI+  AQ+EI AL  +HP  +VMLIAEKGTMG
Sbjct: 180 AEGDISTDLLSPGNQSHSRADRELHGQCMITPEAQQEIVALGKKHPNAKVMLIAEKGTMG 239

Query: 240 VGSSRMSGVNNVALWTGKQASPYVPFVNIAPVVAGTNGISPIFMTTVGVTGGIGIDLKNW 299
           VGSSRMSGVNNVALW G++ SPY+PF+N APVVAGTNGI+PIF+TTVGVTGGIG+DLKNW
Sbjct: 240 VGSSRMSGVNNVALWAGEKTSPYIPFINNAPVVAGTNGIAPIFLTTVGVTGGIGLDLKNW 299

Query: 300 VKKVDGDGNPILNNDGNPILEQKYSVDTGTVLKIDTKARKLMSADGGEELADVSSAFSPQ 359
           VKKVD +GN + + +G+ +LE+ YSV TGTVL IDT A+KL + D  +EL DVS AFSPQ
Sbjct: 300 VKKVDAEGNTVKDANGDNVLEEAYSVATGTVLTIDTAAKKLYNGD--KELVDVSDAFSPQ 357

Query: 360 AVEFMKAGGSYAVVFGKKLQTLAAETLGVEPTPVFAPAKEISHEGQGLTAVEKIFNANAR 419
            VEFMKAGGSYA+ FGKKLQT AAETLG++   VFAP+KEIS EGQGLTAVEKIFN NA 
Sbjct: 358 KVEFMKAGGSYALTFGKKLQTFAAETLGIQAPTVFAPSKEISVEGQGLTAVEKIFNRNAV 417

Query: 420 GVTPGKVLHAGSDVRVQVNIVGSQDTTGLMTSQELEAMAATVLSPTVDGAYQSGCHTASV 479
           GV     LH GSDVRV+VNIVGSQDTTG MT QELE+MAA+ +SP+VDGA+QSGCHTASV
Sbjct: 418 GVASSTPLHTGSDVRVKVNIVGSQDTTGPMTCQELESMAASTISPSVDGAFQSGCHTASV 477

Query: 480 WDLKAQANTPRLMAFMHKFGLITARDPKGVYHSMTDVIHKVLNDITVSDWDIIIGGDSHT 539
           WD KA+ANTP+LMAFM+ FG+ITARDPKGVYHSMTDVIHKVLNDIT+ D  IIIGGDSHT
Sbjct: 478 WDNKAKANTPKLMAFMNDFGVITARDPKGVYHSMTDVIHKVLNDITIDDRAIIIGGDSHT 537

Query: 540 RMSKGVAFGADSGTVALALATGEATMPIPESVKVTFKGKMADHMDFRDVVHATQAQMLAQ 599
           RMSKGVAFGADSGTVA+ALATGE  MPIPESVKVTFKG+M DH+DFRDVVH+TQAQML +
Sbjct: 538 RMSKGVAFGADSGTVAIALATGECAMPIPESVKVTFKGQMKDHIDFRDVVHSTQAQMLNK 597

Query: 600 HGDNVFQGRVIEVHIGTLLADQAFTFTDWTAEMKAKASICISNDDTLIESLEIAKQRIQV 659
            G+NVFQGRVIEV IGTLLADQAFTFTDWTAEMKAKASICIS DDTL++SLE++K RIQ+
Sbjct: 598 FGENVFQGRVIEVQIGTLLADQAFTFTDWTAEMKAKASICISTDDTLVQSLELSKARIQI 657

Query: 660 MIDKGMDNDVQMLAGLIAKANARIAEIRSGEKPALKPDDTARYFAEVVVDLDQIVEPMIA 719
           MI+KGMDN   ML GLI  A+ RIA I+SGE+PAL PDDTA YFAE+VVDLD I EPMIA
Sbjct: 658 MINKGMDNATNMLQGLIDLADKRIAGIQSGEEPALAPDDTATYFAEMVVDLDLIDEPMIA 717

Query: 720 DPDVHNADVSKRYTHDTIRPISYYGAEKKIDLGFVGSCMVHKGDVKIVAQMLRNLEKANG 779
           DPDV+N D SKRYTHD IR  S+Y   +K+DLGFVGSCMVHKGD++I+A MLRNLEK NG
Sbjct: 718 DPDVNNEDASKRYTHDVIRQASFYDG-RKVDLGFVGSCMVHKGDMQIIAAMLRNLEK-NG 775

Query: 780 EVKFKAPLVLAAPTYNIIDELKEEGDWDVLQKYAGFEFDDSAPKEKARTEYENILYLERP 839
            + F +PLV+A PTYNI+DELK EGDW+VL KYAGF FDDS PKE ART+YENI+YLERP
Sbjct: 776 PITFNSPLVVAPPTYNIVDELKAEGDWEVLAKYAGFTFDDSHPKEAARTKYENIMYLERP 835

Query: 840 GCNLCMGNQEKAAKGDTVLATSTRLFQGRVVADSETKKGESLLGSTPVVVLSAILGRTPT 899
           GCNLCMGNQEKA  GDTVLATSTRLFQGRVV DS  KKGESLLGSTP+VVL++ILGR PT
Sbjct: 836 GCNLCMGNQEKAEAGDTVLATSTRLFQGRVVEDSTEKKGESLLGSTPMVVLASILGRFPT 895

Query: 900 VEEYKTAVEGINLTKFAPP----LTPPIDAKSV 928
           + EYK AVEGINLT FAPP      P I  K+V
Sbjct: 896 IAEYKAAVEGINLTSFAPPSEDLARPAIPLKAV 928


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: 2249
Number of extensions: 74
Number of successful extensions: 6
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: 928
Length adjustment: 43
Effective length of query: 887
Effective length of database: 885
Effective search space:   784995
Effective search space used:   784995
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 Apr 09 2024. 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:

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. 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:

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:

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