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_013451188.1 CALNI_RS05335 aconitate hydratase AcnA
Query= SwissProt::Q5SMF6
(902 letters)
>NCBI__GCF_000183405.1:WP_013451188.1
Length = 877
Score = 1001 bits (2588), Expect = 0.0
Identities = 506/881 (57%), Positives = 643/881 (72%), Gaps = 23/881 (2%)
Query: 18 YGYYDLQELERKGVAEVSRLPFSIRVMLESLLRNEDGYQVTREDIEALARW-RPDPGEIN 76
Y +YD+ +L + G ++ +LP+SI++++E++LRN QV +D++ +A W R P I
Sbjct: 17 YFFYDINKLSKDGF-DIKKLPYSIKILVENILRNLGDGQVNEKDLKNIAGWSRKQPIPIE 75
Query: 77 VPLKLARVILQDFTGVPAVVDLAAMRDAIKAKGGDPKRINPVVPADLVIDHSVQVDAFGT 136
+P K RV++QDFTGVPAVVDLAAMRDA+ G +P++INP+VP DL++DHSVQVD +GT
Sbjct: 76 IPYKPVRVLMQDFTGVPAVVDLAAMRDAMLELGKNPEKINPLVPVDLIVDHSVQVDYYGT 135
Query: 137 AYAFFYNVEKEYERNRERYLLLKWAQNALENFRVVPPGTGIVHQVNIEYLTKVVMTGKRD 196
+ NV EY+RN ERY LLKWAQ + NFRVVPP +GI HQVN+EYL KVV R
Sbjct: 136 EDSILKNVALEYKRNEERYKLLKWAQKSFHNFRVVPPNSGICHQVNLEYLAKVVCIDDRK 195
Query: 197 GLTLAFPDSLVGTDSHTTMVNGLGVLGWGVGGIEAEAVMLGQPYYMLAPRVVGFKLYGEL 256
L + D+ +GTDSHT MVNG+GV+GWGVGGIEAEAVMLGQPYYM P V+G KL GEL
Sbjct: 196 DKKLLYLDTCIGTDSHTPMVNGIGVMGWGVGGIEAEAVMLGQPYYMPIPEVIGVKLIGEL 255
Query: 257 PEGATATDLVLTVTEMLRKHGVVGKFVEFYGPGVAKLSTPDRATIANMAPEYGATMGFFP 316
EG TATDL+LT+TE LR++GVV KFVE++GPGV LS PDRATI+NM PE+GAT+G FP
Sbjct: 256 NEGVTATDLILTITEKLRRYGVVDKFVEYFGPGVKTLSIPDRATISNMTPEFGATLGIFP 315
Query: 317 VDEETLNYLRQTGRPEELVELVEAYTKAVGLFRTPEAEEKVQYSEYLELDLSAVEPSLAG 376
+D +T+ YLR T R + +++E Y K G+F T +EKV+Y++ LE+DL+++EPS+AG
Sbjct: 316 IDRKTIEYLRMTNR-DRYADILEIYAKKAGIFYT--GQEKVEYTDVLEIDLNSIEPSIAG 372
Query: 377 PKRPQDRVPLKEVKKSFLAHLTKPVKERGFGLSEDQLQRKVLVKRRDEEFELTHGSVVIA 436
P RPQDR+ L +VK + L + V ++ + GSVVIA
Sbjct: 373 PSRPQDRISLSQVKSN---------------LQNLKTDNFVDIEIDQNPVRIKDGSVVIA 417
Query: 437 AITSCTNTSNPSVMLGAGLLAKKAVEAGLDRKPWVKTSLAPGSKVVTDYLEMSGLMPFLE 496
AITSCTNTSNP V++GAGL+A+ AV+ GL KP+VKTS APGSKVV YL+ SGLMP+LE
Sbjct: 418 AITSCTNTSNPFVIIGAGLMARNAVKKGLRVKPYVKTSFAPGSKVVESYLKKSGLMPYLE 477
Query: 497 ALGFHLVGYGCTTCIGNSGPLPEDIAKAVEEGNLVVAAVLSGNRNFEGRINPHVKANYLA 556
ALGFH+ YGCTTCIGNSGP+ I +A+ + NL VAAVLSGNRNFE RI+ V++N+LA
Sbjct: 478 ALGFHITAYGCTTCIGNSGPVLPQIEEAIIKNNLNVAAVLSGNRNFEARIHQLVRSNFLA 537
Query: 557 SPMLVVAYALAGRMDIDFTTEPLGFDPNGKPIYLKDIWPSMEEIREAIRKTLDPELFKKE 616
SPMLVVAYALAG++DIDF EPLG+ P G+ + LKD+WPS EEI E I T FK++
Sbjct: 538 SPMLVVAYALAGKIDIDFKNEPLGYTPYGEKVMLKDLWPSSEEIHEIISDTFTKSDFKRD 597
Query: 617 YSKVFEGDERWQALPAPTGELYQWDPESTYIQNPPFFEDLGER--KVEDIRGARVLLVLG 674
Y K+F+GD WQ + + Y W +STYI+ PP+F++ + K+ DI AR+LL+LG
Sbjct: 598 YGKIFDGDLFWQKMNVKVDKTYHWHEKSTYIKKPPYFDNFMKEPGKIFDITNARILLLLG 657
Query: 675 DSVTTDHISPAGAIPVKSPAGQYLISKGVKPEDFNSYGSRRGNHEVMMRGTFANIRIKNL 734
DS+TTDHISPAG I PAG+YLISKGVK +DFNSYGSRRGNHEVM+RGTF NIRIKN
Sbjct: 658 DSITTDHISPAGEIDPDYPAGKYLISKGVKEDDFNSYGSRRGNHEVMIRGTFGNIRIKNK 717
Query: 735 MLDGIEGGYAKKLPEGDVDFVYNVAMRYKAEGTPLLVIAGKEYGTGSSRDWAAKGTYLLG 794
M++ EG + K PE + F+++ AM+Y+ E TPL+V AGKEYGTGSSRDWAAKGT LLG
Sbjct: 718 MVNR-EGSFTVKYPENEEMFIFDAAMKYQMENTPLVVFAGKEYGTGSSRDWAAKGTSLLG 776
Query: 795 IRAVLAESFERIHRSNLVGMGVLPLEFLPGENRETLGLTGYEVYDILGLEDLKPRKLVDI 854
I+AV+AESFERIH+SNLVGMG+LPL+F GE+ + G EV I GLE+L PRK + I
Sbjct: 777 IKAVIAESFERIHKSNLVGMGILPLQFKEGESWAKYEIKGDEVVSIFGLENLSPRKDIRI 836
Query: 855 VARREDGSEVRFQAIARLDTPVEVDYYKNGGILQTVLLNML 895
+ DG + F RLDT VEV+YY NGGIL VL L
Sbjct: 837 ELSKPDGEKREFFVTLRLDTEVEVEYYANGGILPYVLRRFL 877
Lambda K H
0.317 0.137 0.399
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: 2223
Number of extensions: 96
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: 902
Length of database: 877
Length adjustment: 43
Effective length of query: 859
Effective length of database: 834
Effective search space: 716406
Effective search space used: 716406
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)
Align candidate WP_013451188.1 CALNI_RS05335 (aconitate hydratase AcnA)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR01341.hmm
# target sequence database: /tmp/gapView.3244277.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01341 [M=876]
Accession: TIGR01341
Description: aconitase_1: aconitate hydratase 1
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1330.3 0.1 0 1330.1 0.1 1.0 1 NCBI__GCF_000183405.1:WP_013451188.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000183405.1:WP_013451188.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1330.1 0.1 0 0 2 876 .] 16 877 .] 15 877 .] 0.98
Alignments for each domain:
== domain 1 score: 1330.1 bits; conditional E-value: 0
TIGR01341 2 kvyyyslkaleeslekisklpkslrillesvlrnldgskikeedveallkwkkeelkdeeiafkparvvlqdf 74
++++y +++l++++ +i+klp+s++il+e++lrnl + +++e+d+++++ w++++ +ei++kp rv++qdf
NCBI__GCF_000183405.1:WP_013451188.1 16 EYFFYDINKLSKDGFDIKKLPYSIKILVENILRNLGDGQVNEKDLKNIAGWSRKQPIPIEIPYKPVRVLMQDF 88
689********************************************************************** PP
TIGR01341 75 tGvpavvdlaalreavknlgkdpekinplvpvdlvidhsvqvdkageeealeanvelefernkerykflkwak 147
tGvpavvdlaa+r+a+ +lgk+pekinplvpvdl++dhsvqvd++g+e+++ +nv le++rn+eryk+lkwa+
NCBI__GCF_000183405.1:WP_013451188.1 89 TGVPAVVDLAAMRDAMLELGKNPEKINPLVPVDLIVDHSVQVDYYGTEDSILKNVALEYKRNEERYKLLKWAQ 161
************************************************************************* PP
TIGR01341 148 kafknlkvvppgtGivhqvnleylakvvfeaekdgellaypdslvGtdshttminGlGvlGwGvGGieaeaal 220
k+f+n++vvpp +Gi+hqvnleylakvv +++ ++l+y d+ +Gtdsht m+nG+Gv+GwGvGGieaea++
NCBI__GCF_000183405.1:WP_013451188.1 162 KSFHNFRVVPPNSGICHQVNLEYLAKVVCIDDRKDKKLLYLDTCIGTDSHTPMVNGIGVMGWGVGGIEAEAVM 234
************************************************************************* PP
TIGR01341 221 lGqpvslsvpeviGvkltGklreGvtatdlvltvtellrkkgvvgkfveffGeglkelsladratianmapey 293
lGqp+++ +peviGvkl G+l+eGvtatdl+lt+te lr+ gvv+kfve+fG+g+k+ls++drati+nm+pe+
NCBI__GCF_000183405.1:WP_013451188.1 235 LGQPYYMPIPEVIGVKLIGELNEGVTATDLILTITEKLRRYGVVDKFVEYFGPGVKTLSIPDRATISNMTPEF 307
************************************************************************* PP
TIGR01341 294 GataaffpiddvtlqylrltgrdedkvelvekylkaqelfvddseepkytdvveldlsdveasvaGpkrpqdr 366
Gat ++fpid +t++ylr+t+rd +++e y+k ++f++ e+++ytdv+e+dl+++e+s+aGp rpqdr
NCBI__GCF_000183405.1:WP_013451188.1 308 GATLGIFPIDRKTIEYLRMTNRDR-YADILEIYAKKAGIFYTGQEKVEYTDVLEIDLNSIEPSIAGPSRPQDR 379
***********************9.99********************************************** PP
TIGR01341 367 valkevkaafksslesnagekglalrkeakekklegkeaelkdgavviaaitsctntsnpsvllgagllakka 439
++l++vk++ l++ +++ ++ ++++ ++kdg+vviaaitsctntsnp v++gagl+a+ a
NCBI__GCF_000183405.1:WP_013451188.1 380 ISLSQVKSN----LQNLKTDNF-------VDIEIDQNPVRIKDGSVVIAAITSCTNTSNPFVIIGAGLMARNA 441
******984....444444444.......45566778899********************************* PP
TIGR01341 440 velGlkvkpyvktslapGskvvtdylaesgllpyleelGfnlvGyGcttciGnsGpleeeveeaikendlevs 512
v+ Gl+vkpyvkts apGskvv yl++sgl+pyle+lGf++ yGcttciGnsGp+ ++eeai +n+l+v+
NCBI__GCF_000183405.1:WP_013451188.1 442 VKKGLRVKPYVKTSFAPGSKVVESYLKKSGLMPYLEALGFHITAYGCTTCIGNSGPVLPQIEEAIIKNNLNVA 514
************************************************************************* PP
TIGR01341 513 avlsGnrnfegrihplvkanylaspplvvayalaGtvdidlekepigtdkdGkkvylkdiwpsakeiaelvkk 585
avlsGnrnfe+rih+lv++n+lasp+lvvayalaG++did+++ep+g+ G+kv lkd+wps +ei+e++++
NCBI__GCF_000183405.1:WP_013451188.1 515 AVLSGNRNFEARIHQLVRSNFLASPMLVVAYALAGKIDIDFKNEPLGYTPYGEKVMLKDLWPSSEEIHEIISD 587
************************************************************************* PP
TIGR01341 586 avkkelfkkeyeevtegnerwnelevtssdlyewdekstyireppffeelklepeevedikgarillllGdsi 658
+ +k fk++y ++++g+ w++++v +++y+w+ekstyi++pp+f+++ ep ++ di++arillllGdsi
NCBI__GCF_000183405.1:WP_013451188.1 588 TFTKSDFKRDYGKIFDGDLFWQKMNVKVDKTYHWHEKSTYIKKPPYFDNFMKEPGKIFDITNARILLLLGDSI 660
************************************************************************* PP
TIGR01341 659 ttdhispaGsikkdspaakylkekGverrdfnsyGsrrGnhevmlrGtfaniriknklvkgkeGgltvylpds 731
ttdhispaG i++d pa+kyl+ kGv++ dfnsyGsrrGnhevm+rGtf niriknk+v+ +eG++tv +p++
NCBI__GCF_000183405.1:WP_013451188.1 661 TTDHISPAGEIDPDYPAGKYLISKGVKEDDFNSYGSRRGNHEVMIRGTFGNIRIKNKMVN-REGSFTVKYPEN 732
************************************************************.************ PP
TIGR01341 732 evvsvydaamkykkegvplvvlaGkeyGsGssrdwaakgtkllGvkaviaesferihrsnlvgmGvlplefkq 804
e++ ++daamky+ e++plvv aGkeyG+Gssrdwaakgt+llG+kaviaesferih+snlvgmG+lpl+fk+
NCBI__GCF_000183405.1:WP_013451188.1 733 EEMFIFDAAMKYQMENTPLVVFAGKEYGTGSSRDWAAKGTSLLGIKAVIAESFERIHKSNLVGMGILPLQFKE 805
************************************************************************* PP
TIGR01341 805 gedaetlgltgeetidvddieelkpkkevtvelvkedgeketveavlridtevelayvkkgGilqyvlrkll 876
ge+ +++g+e + + ++e+l+p+k++++el k dgek+ + ++lr+dteve++y+ +gGil yvlr++l
NCBI__GCF_000183405.1:WP_013451188.1 806 GESWAKYEIKGDEVVSIFGLENLSPRKDIRIELSKPDGEKREFFVTLRLDTEVEVEYYANGGILPYVLRRFL 877
*********************************************************************986 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (876 nodes)
Target sequences: 1 (877 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 36.86
//
[ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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:
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