GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acn in Klebsiella michiganensis M5al

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate BWI76_RS11940 BWI76_RS11940 aconitate hydratase 1

Query= SwissProt::Q8ZP52
         (891 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS11940 BWI76_RS11940 aconitate
           hydratase 1
          Length = 890

 Score = 1594 bits (4128), Expect = 0.0
 Identities = 781/890 (87%), Positives = 842/890 (94%)

Query: 1   MSSTLREASKDTLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTD 60
           MSSTLR ASKDTLQ KDKT+HYYSLPLAAK LGD++RLPKSLKVLLENLLRWQDG+SVT 
Sbjct: 1   MSSTLRAASKDTLQVKDKTWHYYSLPLAAKQLGDLSRLPKSLKVLLENLLRWQDGDSVTA 60

Query: 61  EDIQALAGWLKNAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPL 120
           EDI ALAGWLK+AHADREIA+RPARVLMQDFTGVPAVVDLAAMREAVKRLGGDT+KVNPL
Sbjct: 61  EDIHALAGWLKHAHADREIAYRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTAKVNPL 120

Query: 121 SPVDLVIDHSVTVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGIC 180
           SPVDLVIDHSVTVD FGDDDAFEENVRLEMERNHERY+FL+WG+QAFSRFSVVPPGTGIC
Sbjct: 121 SPVDLVIDHSVTVDRFGDDDAFEENVRLEMERNHERYVFLRWGQQAFSRFSVVPPGTGIC 180

Query: 181 HQVNLEYLGKAVWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240
           HQVNLEYLG+AVWSE Q+GEW+A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ
Sbjct: 181 HQVNLEYLGRAVWSEQQNGEWVAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQ 240

Query: 241 PVSMLIPDVVGFKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300
           PVSMLIPDVVGFKL+GKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR
Sbjct: 241 PVSMLIPDVVGFKLSGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADR 300

Query: 301 ATIANMSPEYGATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFT 360
           ATIANMSPEYGATCGFFPIDA+TL+YMRL+GRS++ V LVE YAKAQGMWR PGDEPVFT
Sbjct: 301 ATIANMSPEYGATCGFFPIDAVTLDYMRLTGRSEEQVALVEAYAKAQGMWRQPGDEPVFT 360

Query: 361 STLELDMGDVEASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPVDYTMNGQPY 420
           STL LDMG VEASLAGPKRPQDRVALGDVP+AFAAS+ELE+N AQ+D++P+DYT+NGQ Y
Sbjct: 361 STLALDMGTVEASLAGPKRPQDRVALGDVPQAFAASSELEVNHAQKDKRPIDYTLNGQQY 420

Query: 421 QLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYL 480
            LPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAV  GLK QPWVKASLAPGSKVVSDYL
Sbjct: 421 SLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVERGLKPQPWVKASLAPGSKVVSDYL 480

Query: 481 AQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSGNRNFEGRI 540
           A AKLTP+LDELGFNLVGYGCTTCIGNSGPLP+PIE AIK+GDLTVGAVLSGNRNFEGRI
Sbjct: 481 AHAKLTPWLDELGFNLVGYGCTTCIGNSGPLPDPIERAIKQGDLTVGAVLSGNRNFEGRI 540

Query: 541 HPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQEIARAVEL 600
           HPLVKTNWLASPPLVVAYALAGNMN++L  +PLG  + G PVYLKDIWPS  E+A+AVE 
Sbjct: 541 HPLVKTNWLASPPLVVAYALAGNMNLDLTREPLGTGKDGQPVYLKDIWPSGIEVAQAVEQ 600

Query: 601 VSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQPAPVKDIH 660
           VS++MFRKEYAEVFEGT EWK+I+V+ SDTY WQ+DSTYIRLSPFFDEM  +P PV+DIH
Sbjct: 601 VSTEMFRKEYAEVFEGTAEWKAIKVDRSDTYDWQNDSTYIRLSPFFDEMGVEPKPVEDIH 660

Query: 661 GARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGNHEVMMRGT 720
           GARILAMLGDSVTTDHISPAGSIK DSPAGRYLQNHGVER DFNSYGSRRGNHEVMMRGT
Sbjct: 661 GARILAMLGDSVTTDHISPAGSIKADSPAGRYLQNHGVERIDFNSYGSRRGNHEVMMRGT 720

Query: 721 FANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEYGSGSSRDW 780
           FANIRIRNEM+PGVEGGMTRHLP T+ ++IYDAAMLY++E TPLAVIAGKEYGSGSSRDW
Sbjct: 721 FANIRIRNEMVPGVEGGMTRHLPDTQPIAIYDAAMLYKEEGTPLAVIAGKEYGSGSSRDW 780

Query: 781 AAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEVIDIADLQN 840
           AAKGPRLLG+RVVIAESFERIHRSNLIGMGILPLEFPQG+TRKTLGL GEE IDI++LQ 
Sbjct: 781 AAKGPRLLGVRVVIAESFERIHRSNLIGMGILPLEFPQGMTRKTLGLNGEERIDISNLQA 840

Query: 841 LRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890
           L+PG T+PVTLTR+DG +E + CRCRIDTATELTYYQNDGILHYVIRNML
Sbjct: 841 LQPGMTVPVTLTRADGRQEVIDCRCRIDTATELTYYQNDGILHYVIRNML 890


Lambda     K      H
   0.317    0.135    0.401 

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: 2468
Number of extensions: 100
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: 891
Length of database: 890
Length adjustment: 43
Effective length of query: 848
Effective length of database: 847
Effective search space:   718256
Effective search space used:   718256
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: 56 (26.2 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:

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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