GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Marinicella litoralis KMM 3900

Align Aconitate hydratase A; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_099018782.1 CCS90_RS06680 aconitate hydratase AcnA

Query= SwissProt::O53166
         (943 letters)



>NCBI__GCF_002591915.1:WP_099018782.1
          Length = 933

 Score =  946 bits (2445), Expect = 0.0
 Identities = 477/948 (50%), Positives = 658/948 (69%), Gaps = 24/948 (2%)

Query: 1   MTSKSVNSFGAHDTLKVGEKSYQIYRLDAVPNTA----KLPYSLKVLAENLLRNEDGSNI 56
           M +  ++ F A   L++G + ++ + L A+        KLP+S+++L EN +RN DG  +
Sbjct: 1   MNTLDLDPFKAKKILQIGAEEHEYFSLKALQKQGYAIEKLPFSIRILLENAVRNFDGFGV 60

Query: 57  TKDHIEAIANWDPKAEPSIEIQYTPARVVMQDFTGVPCIVDLATMREAIADLGGNPDKVN 116
           TK HIE + NW PK     +I + PARV+MQDFTGVP +VDLA +R  +A  G   D +N
Sbjct: 61  TKAHIETLLNWQPKGGTD-DIPFKPARVLMQDFTGVPAVVDLAAIRAEVARKGKQVDLIN 119

Query: 117 PLAPADLVIDHSVIADLFGRADAFERNVEIEYQRNGERYQFLRWGQGAFDDFKVVPPGTG 176
           PL P DLVIDHSV  D FG  D+++RN+E+EY RN ERYQ L+W Q AF +F VVPPG G
Sbjct: 120 PLIPVDLVIDHSVQIDYFGTEDSYQRNIELEYSRNRERYQLLKWAQNAFTNFSVVPPGMG 179

Query: 177 IVHQVNIEYLASVVMTRDGVAYPDTCVGTDSHTTMVNGLGVLGWGVGGIEAEAAMLGQPV 236
           I HQVN+EYL+  V+ RDG  +PDT VGTDSHT MVNG+GV+GWGVGGIEAEAA+LGQP+
Sbjct: 180 ICHQVNLEYLSQGVIARDGQLFPDTLVGTDSHTPMVNGIGVVGWGVGGIEAEAAILGQPI 239

Query: 237 SMLIPRVVGFRLTGEIQPGVTATDVVLTVTEMLRQHGVVGKFVEFYGEGVAEVPLANRAT 296
             ++P V+G +L+G +  G TATD+VLTV E+LR HGVVGKFVE +G+G+  + + +RAT
Sbjct: 240 YFIMPEVIGLKLSGTLPVGSTATDLVLTVAELLRTHGVVGKFVEVFGQGLDTLSVPDRAT 299

Query: 297 LGNMSPEFGSTAAIFPIDEETIKYLRFTGRTPEQVALVEAYAKAQGMWHDPKHEPEFSEY 356
           LGNMSPEFG T   FPID++T++Y+R + R+ EQ+  VE Y K   +W + +    ++  
Sbjct: 300 LGNMSPEFGCTITYFPIDDKTLEYMRNSNRSDEQIERVERYCKENMLWRENEEAINYTTV 359

Query: 357 LELNLSDVVPSIAGPKRPQDRIALAQAKSTFREQIYHYVGNGSPDSPHDPHSKLDEVVEE 416
           LEL++S + P+IAGPK PQ +I L  AK+ F E ++   G    +   +   + +E +E+
Sbjct: 360 LELDVSGIKPTIAGPKLPQQKILLENAKAKFGELLHGGFGRSYVE---EKDRETEEELEK 416

Query: 417 TFPASDPGQLTFANDDVATDETVHSAAAHADGRVSNPVRV--KSDELGEFVLDHGAVVIA 474
            F      Q+  +N+D  T + +H       G+  N ++     +E  ++ L  G++ IA
Sbjct: 417 RFVDEGGDQIEKSNED-KTIKQIHR------GKTINGLKSVWVDEERLKYKLADGSIAIA 469

Query: 475 AITSCTNTSNPEVMLGAALLARNAVEKGLTSKPWVKTTIAPGSQVVNDYYDRSGLWPYLE 534
           AITSCTNTSNP VM+GA L+ARNA++KG+  KPWVKT++APGS+VV DY +++GL    E
Sbjct: 470 AITSCTNTSNPFVMIGAGLVARNAIKKGIDVKPWVKTSLAPGSKVVTDYLNKAGLMTDFE 529

Query: 535 KLGFYLVGYGCTTCIGNSGPLPEEISKAVNDNDLSVTAVLSGNRNFEGRINPDVKMNYLA 594
            L F+LVGYGCT+CIGNSGPL   + +AV D DL VT+VLSGNRNFE RI+P VKMN+L 
Sbjct: 530 ALQFHLVGYGCTSCIGNSGPLLPAVEQAVKDYDLVVTSVLSGNRNFEARIHPLVKMNFLM 589

Query: 595 SPPLVIAYALAGTMDFDFQTQPLGQDKDGKNVFLRDIWPSQQDVSDTIAAAINQEMFTRN 654
           SP LV+A+ALAG +D D + + LG  ++G  V+LRDIWPS  +++  +A  +  + F +N
Sbjct: 590 SPMLVVAFALAGRVDIDMENEALGHTRNGDPVYLRDIWPSDDEINAIMAEVLTPKYFAKN 649

Query: 655 YADVFKGDDRWRNLPTPSGNTFEWDPNSTYVRKPPYFEGMTAKPEPVGNISGARVLALLG 714
           Y ++F G+  W+++P   GN ++W+ +STY+++ P+F+ +  +P  + NI  AR L  LG
Sbjct: 650 YGEIFAGNQIWQDMPVAKGNLYQWEESSTYIQEIPFFKDLPEQPAAMQNIIDARALLKLG 709

Query: 715 DSVTTDHISPAGAIKPGTPAARYLDEHGVDRKDYNSFGSRRGNHEVMIRGTFANIRLRNQ 774
           D+ +TDHISPAG+    + A +YL   GV R D+NS+GSRRGN EVM+RGTFAN+R++NQ
Sbjct: 710 DNTSTDHISPAGSFNETSAAGQYLISKGVKRADFNSYGSRRGNDEVMLRGTFANVRIKNQ 769

Query: 775 LLDDVSGGYTRDFTQPGGPQAFIYDAAQNYAAQHIPLVVFGGKEYGSGSSRDWAAKGTLL 834
           L+ +  GG T     P   +  +Y+AA+ Y   +IPLVV GGKEYGSGSSRDWAAKGT L
Sbjct: 770 LV-ETEGGVT--LYLPTQEEMSVYEAAKKYRENNIPLVVLGGKEYGSGSSRDWAAKGTSL 826

Query: 835 LGVRAVIAESFERIHRSNLIGMGVIPLQFPEGKSASSLGLDGTEVFDITGIDVLNDGKTP 894
           LGV+AV+ +S+ERIHRSNL+ MGV+PLQ+  G++A SL LDGTE F+ITGI    +G  P
Sbjct: 827 LGVKAVLVDSYERIHRSNLVYMGVLPLQYLPGQNADSLSLDGTETFNITGI---AEGLEP 883

Query: 895 -KTVCVQATKGDGATIEFDAVVRIDTPGEADYYRNGGILQYVLRNILK 941
            K V V+A K DG  + F+A  R+D+  E  YY++GGILQYVLR+ LK
Sbjct: 884 RKKVSVKAIKADGEVVSFEAEARLDSAIEVAYYQHGGILQYVLRDFLK 931


Lambda     K      H
   0.316    0.136    0.403 

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: 113
Number of successful extensions: 5
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: 943
Length of database: 933
Length adjustment: 43
Effective length of query: 900
Effective length of database: 890
Effective search space:   801000
Effective search space used:   801000
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.

Links

Downloads

Related tools

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