GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Koxy:BWI76_RS11940
          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:

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