GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_2301 Aconitate hydratase (EC 4.2.1.3)

Query= SwissProt::Q8ZP52
         (891 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2301
          Length = 913

 Score = 1259 bits (3259), Expect = 0.0
 Identities = 621/900 (69%), Positives = 730/900 (81%), Gaps = 21/900 (2%)

Query: 12  TLQAKDKTYHYYSLPLAAKSLGDIARLPKSLKVLLENLLRWQDGESVTDEDIQALAGWLK 71
           TLQ   +TYHY+SLP AA+SLGD+ +LP SLKVLLENLLRW+D ++VT  D++ALAGWLK
Sbjct: 12  TLQVDARTYHYFSLPEAARSLGDLDKLPMSLKVLLENLLRWEDEKTVTGTDLKALAGWLK 71

Query: 72  NAHADREIAWRPARVLMQDFTGVPAVVDLAAMREAVKRLGGDTSKVNPLSPVDLVIDHSV 131
              +DREI +RPARVLMQDFTGVPAVVDLAAMR AV++ GGD  ++NPLSPVDLVIDHSV
Sbjct: 72  ERRSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAVEKAGGDPQRINPLSPVDLVIDHSV 131

Query: 132 TVDHFGDDDAFEENVRLEMERNHERYMFLKWGKQAFSRFSVVPPGTGICHQVNLEYLGKA 191
            VD F    AFE+NV +EM+RN ERY FL+WG+ AF  FSVVPPGTGICHQVNLEYLG+ 
Sbjct: 132 MVDKFASSQAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQVNLEYLGRT 191

Query: 192 VWSELQDGEWIAYPDSLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVG 251
           VW++ +DG   A+PD+LVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIP+V+G
Sbjct: 192 VWTKEEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPEVIG 251

Query: 252 FKLTGKLREGITATDLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYG 311
           FKLTGKLREGITATDLVLTVTQMLRK GVVGKFVEFYGDGL  LPLADRATIANM+PEYG
Sbjct: 252 FKLTGKLREGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRATIANMAPEYG 311

Query: 312 ATCGFFPIDAITLEYMRLSGRSDDLVELVETYAKAQGMWRNPGDEPVFTSTLELDMGDVE 371
           ATCGFFP+D +TL+Y+RLSGR  + V+LVE Y KAQG+WR PG EPVFT TLELDMG VE
Sbjct: 312 ATCGFFPVDEVTLDYLRLSGRPAETVKLVEAYCKAQGLWRLPGQEPVFTDTLELDMGSVE 371

Query: 372 ASLAGPKRPQDRVALGDVPKAFAASAELELNTAQRDRQPVD------------------- 412
           ASLAGPKRPQDRV+L +V +AF+    L++    ++   ++                   
Sbjct: 372 ASLAGPKRPQDRVSLPNVGQAFSDFLGLQVKPTSKEEGRLESEGGGGVAVGNADQVGEAE 431

Query: 413 YTMNGQPYQLPDGAVVIAAITSCTNTSNPSVLMAAGLLAKKAVTLGLKRQPWVKASLAPG 472
           Y   G  ++L +GAVVIAAITSCTNTSNPSV+MAAGLLAKKAV  GL R+PWVK+SLAPG
Sbjct: 432 YEFEGHTHRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLTRKPWVKSSLAPG 491

Query: 473 SKVVSDYLAQAKLTPYLDELGFNLVGYGCTTCIGNSGPLPEPIETAIKKGDLTVGAVLSG 532
           SKVV+DY   A LT YLD+LGF+LVGYGCTTCIGNSGPLPEPIE AI+K DLTV +VLSG
Sbjct: 492 SKVVTDYYKAAGLTEYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQKADLTVASVLSG 551

Query: 533 NRNFEGRIHPLVKTNWLASPPLVVAYALAGNMNINLATDPLGYDRKGDPVYLKDIWPSAQ 592
           NRNFEGR+HPLVKTNWLASPPLVVAYALAG + I+++++PLG DR G PVYL+D+WPS+Q
Sbjct: 552 NRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDRDGKPVYLRDVWPSSQ 611

Query: 593 EIARAVELVSSDMFRKEYAEVFEGTEEWKSIQVESSDTYGWQSDSTYIRLSPFFDEMQAQ 652
           E+A AV  V++ MF KEYA VF G E+W++I+V  + TY WQ DSTYI+  PFFD +   
Sbjct: 612 EVATAVAQVNTSMFHKEYAAVFAGDEQWQAIEVPQAATYVWQDDSTYIQHPPFFDAIDGP 671

Query: 653 PAPVKDIHGARILAMLGDSVTTDHISPAGSIKPDSPAGRYLQNHGVERKDFNSYGSRRGN 712
           P  VK++ GARILA+LGDSVTTDHISPAG+IK DSPAGRYL+  GVE +DFNSYGSRRGN
Sbjct: 672 PPAVKNVEGARILALLGDSVTTDHISPAGNIKADSPAGRYLREQGVEPRDFNSYGSRRGN 731

Query: 713 HEVMMRGTFANIRIRNEMLPGVEGGMTRHLPGTEAMSIYDAAMLYQQEKTPLAVIAGKEY 772
           H+VMMRGTFANIRIRNEML G EGG T ++P  E M IYDAAMLYQ   TPL VIAG+EY
Sbjct: 732 HQVMMRGTFANIRIRNEMLDGEEGGNTIYIPSGERMPIYDAAMLYQAVGTPLVVIAGQEY 791

Query: 773 GSGSSRDWAAKGPRLLGIRVVIAESFERIHRSNLIGMGILPLEFPQGVTRKTLGLTGEEV 832
           G+GSSRDWAAKG  LLG++ VIAESFERIHRSNL+GMG+LPL+F     RK+L LTG+E 
Sbjct: 792 GTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQNRKSLNLTGKET 851

Query: 833 IDIADLQN--LRPGATIPVTLTRSDGSKETVPCRCRIDTATELTYYQNDGILHYVIRNML 890
           +DI  L +  L P   +P+ +TR DGS+E +   CRIDT  E+ Y++  GILHYV+R ++
Sbjct: 852 LDILGLNDVELTPRMNLPLVITREDGSQERIEVLCRIDTLNEVEYFKAGGILHYVLRQLI 911


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: 2235
Number of extensions: 90
Number of successful extensions: 3
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: 913
Length adjustment: 43
Effective length of query: 848
Effective length of database: 870
Effective search space:   737760
Effective search space used:   737760
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