Alignments for a candidate for carB in Thermocrinis albus DSM 14484

GapMind for Amino acid biosynthesis

Alignments for a candidate for carB in Thermocrinis albus DSM 14484

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate WP_012992546.1 THAL_RS07680 carbamoyl-phosphate synthase large subunit

Query= SwissProt::Q42601
         (1187 letters)



>NCBI__GCF_000025605.1:WP_012992546.1
          Length = 557

 Score =  676 bits (1745), Expect = 0.0
 Identities = 343/546 (62%), Positives = 425/546 (77%), Gaps = 6/546 (1%)

Query: 94  KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
           KR D+KKI+I+G+GPIVIGQA EFDYSGTQACKAL EEGY+V+L+NSNPATIMTDP  A+
Sbjct: 3   KRKDIKKILIIGSGPIVIGQAAEFDYSGTQACKALVEEGYQVVLVNSNPATIMTDPGMAH 62

Query: 154 RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
           RTYI P+T +++E++I+ ERPDALLPT+GGQTALNLAV L E G LE+YGVEL+GA   A
Sbjct: 63  RTYIEPLTVDILEEIIKVERPDALLPTLGGQTALNLAVKLYEEGVLERYGVELLGASYTA 122

Query: 214 IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
           IKK EDR+LFK +M+ IGLK PPS + ++L+E     ++IG FP I+RPAFTLGGTGG I
Sbjct: 123 IKKGEDRQLFKKSMERIGLKVPPSAVVSSLEEALQAIKEIG-FPAILRPAFTLGGTGGAI 181

Query: 274 AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
           AYN EEF    +  L  S   QVL++KSL+GWKEYE EV+RD  DNV+I+CSIEN DPMG
Sbjct: 182 AYNMEEFVERLQIALKTSPIHQVLIDKSLIGWKEYEFEVVRDRKDNVIIVCSIENFDPMG 241

Query: 334 VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
           VHTGDSITVAPAQTLTD+EYQ LRD  I I+RE+GV+ GGSN+QFAVNP +G+  +IEMN
Sbjct: 242 VHTGDSITVAPAQTLTDKEYQILRDACIQIMREVGVDTGGSNIQFAVNPENGDFYVIEMN 301

Query: 394 PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
           PRVSRSSALASKATGFPIAK+AAKL+VGYTLD++ NDITR TPASFEPSIDYVV KIPRF
Sbjct: 302 PRVSRSSALASKATGFPIAKVAAKLAVGYTLDELRNDITRHTPASFEPSIDYVVVKIPRF 361

Query: 454 AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
            F KFP +   LTT MKSVGE MA+GRTF+E+F KA+RSLE     +G   +   +   +
Sbjct: 362 DFAKFPEADRTLTTMMKSVGEVMAIGRTFKEAFLKAVRSLE--MDRFGLTTLSMNNLHDE 419

Query: 514 QLKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQYLMSGTLS 573
            LK  LR PNPDRI  I  A ++G  ++E+++L+ +DKWFL Q+ ELV+ E+      +S
Sbjct: 420 DLKRMLRTPNPDRIWHIAEAFRRGWHVEEVHQLTYIDKWFLYQIWELVEFEKLWKDAPIS 479

Query: 574 EITKEDLYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAEFEAHTPY 633
           E   E L + K+ GFSD+++A      EE++R+ R S  ++PS+K VDTCA EF A+TPY
Sbjct: 480 E---ELLRKAKELGFSDRELAQMKGMKEEDIRSLRYSYRIIPSFKGVDTCAGEFVAYTPY 536

Query: 634 MYSSYD 639
            YSSY+
Sbjct: 537 YYSSYE 542



 Score =  230 bits (586), Expect = 3e-64
 Identities = 143/430 (33%), Positives = 228/430 (53%), Gaps = 27/430 (6%)

Query: 650  KKVLILGGGPNRIGQGIEFDYCCCHTSFALQDAGYETIMLNSNPETVSTDYDTSDRLYFE 709
            KK+LI+G GP  IGQ  EFDY       AL + GY+ +++NSNP T+ TD   + R Y E
Sbjct: 8    KKILIIGSGPIVIGQAAEFDYSGTQACKALVEEGYQVVLVNSNPATIMTDPGMAHRTYIE 67

Query: 710  PLTIEDVLNVIDLEKPDGIIVQFGGQTPLKLALPI--KHYLDKHMPMSLSGAGPVRIWGT 767
            PLT++ +  +I +E+PD ++   GGQT L LA+ +  +  L+++          V + G 
Sbjct: 68   PLTVDILEEIIKVERPDALLPTLGGQTALNLAVKLYEEGVLERY---------GVELLGA 118

Query: 768  SPDSIDAAEDRERFNAILDELKIEQPKGGIAKSEADALAIAKEVGYPVVVRPSYVLGGRA 827
            S  +I   EDR+ F   ++ + ++ P   +  S  +AL   KE+G+P ++RP++ LGG  
Sbjct: 119  SYTAIKKGEDRQLFKKSMERIGLKVPPSAVVSSLEEALQAIKEIGFPAILRPAFTLGGTG 178

Query: 828  MEIVYDDSRLITYLENAVQVDPERPVLVDKYLSDAIEIDVDTLTDSYGNVVIGGIMEHIE 887
              I Y+    +  L+ A++  P   VL+DK L    E + + + D   NV+I   +E+ +
Sbjct: 179  GAIAYNMEEFVERLQIALKTSPIHQVLIDKSLIGWKEYEFEVVRDRKDNVIIVCSIENFD 238

Query: 888  QAGVHSGDSACMLPTQTIPASCLQTIRTWTTKLAKKLNV-CGLMNCQYAIT-TSGDVFLL 945
              GVH+GDS  + P QT+     Q +R    ++ +++ V  G  N Q+A+   +GD +++
Sbjct: 239  PMGVHTGDSITVAPAQTLTDKEYQILRDACIQIMREVGVDTGGSNIQFAVNPENGDFYVI 298

Query: 946  EANPRASRTVPFVSKAIGHPLAKYAALVMSGKSLKDL----------NFEKEVIPKHVSV 995
            E NPR SR+    SKA G P+AK AA +  G +L +L          +FE  +   +V V
Sbjct: 299  EMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELRNDITRHTPASFEPSI--DYVVV 356

Query: 996  KEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQIAAGQKLPLSGTVFLSLN 1055
            K   F F KF   D  L   M+S GEVM+I   F  AF  A      ++   G   LS+N
Sbjct: 357  KIPRFDFAKFPEADRTLTTMMKSVGEVMAIGRTFKEAFLKA--VRSLEMDRFGLTTLSMN 414

Query: 1056 DMTKPHLEKI 1065
            ++    L+++
Sbjct: 415  NLHDEDLKRM 424


Lambda     K      H
   0.317    0.133    0.383 

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: 1648
Number of extensions: 76
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1187
Length of database: 557
Length adjustment: 41
Effective length of query: 1146
Effective length of database: 516
Effective search space:   591336
Effective search space used:   591336
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 (21.7 bits)
S2: 56 (26.2 bits)

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 3; EC 6.3.5.5 (characterized)
to candidate WP_012991206.1 THAL_RS00805 carbamoyl-phosphate synthase large subunit

Query= SwissProt::Q42601
         (1187 letters)



>NCBI__GCF_000025605.1:WP_012991206.1
          Length = 532

 Score =  526 bits (1356), Expect = e-153
 Identities = 276/546 (50%), Positives = 373/546 (68%), Gaps = 34/546 (6%)

Query: 650  KKVLILGGGPNRIGQGIEFDYCCCHTSFALQDAGYETIMLNSNPETVSTDYDTSDRLYFE 709
            KKV+ILG GPNRIGQGIEFDY C    F+L++ G +TIM+N NPETVSTDYDT+DRLYFE
Sbjct: 2    KKVVILGSGPNRIGQGIEFDYACVQAIFSLREEGVQTIMINCNPETVSTDYDTADRLYFE 61

Query: 710  PLTIEDVLNVIDLEKPDGIIVQFGGQTPLKLALPIKHYLDKHMPMSLSGAGPVRIWGTSP 769
            P+ +E+VL VI  EKPDG+++QFGGQTPLKL+LP++             AG V I GT P
Sbjct: 62   PVVLENVLEVIRREKPDGVLIQFGGQTPLKLSLPLR------------DAG-VTILGTPP 108

Query: 770  DSIDAAEDRERFNAILDELKIEQPKGGIAKSEADALAIAKEVGYPVVVRPSYVLGGRAME 829
            +SID AEDRE F  ++ +L + QP     +S+ +A+ +A+ +GYPV+VRPSYVLGGRAM 
Sbjct: 109  ESIDIAEDRELFRRLIQKLGLRQPPSEAVRSKEEAIRVAEAIGYPVLVRPSYVLGGRAMR 168

Query: 830  IVYDDSRLITYLENAVQVDPERPVLVDKYLSDAIEIDVDTLTDSYGNVVIGGIMEHIEQA 889
            I+YD   L+TYLE AV+V  +RP+L+D YLSD++E+DVD + D   + ++G +MEHIE+A
Sbjct: 169  IIYDREELVTYLEEAVEVSYQRPILIDAYLSDSVEVDVDAIGDG-EDFLVGAVMEHIEEA 227

Query: 890  GVHSGDSACMLPTQTIPASCLQTIRTWTTKLAKKLNVCGLMNCQYAITTSGDVFLLEANP 949
            GVHSGDSA  +P  T+P+  ++ I+  + ++A+ L V GL+N Q+A+   G+V++LE NP
Sbjct: 228  GVHSGDSAASIPPYTLPSDVVEEIKRQSKEIARSLGVVGLINLQFAV-KDGEVYVLEVNP 286

Query: 950  RASRTVPFVSKAIGHPLAKYAALVMSGKSLKDLNFE-------------KEVIPKH---V 993
            RASRTVPFVSKAIG+PLAK AA V  G+ L++L  E              + +P      
Sbjct: 287  RASRTVPFVSKAIGYPLAKLAAKVSIGRKLRELVPEVFRRLEEGNVHPCSDFLPSDWNLY 346

Query: 994  SVKEAVFPFEKFQGCDVILGPEMRSTGEVMSISSEFSSAFAMAQIAAGQKLPLSGTVFLS 1053
             VKE VFP+ +F   D +LGPEM+STGEVM I + F  AF  AQ+A G +LP  G+VF+S
Sbjct: 347  CVKEVVFPWNRFPEVDPVLGPEMKSTGEVMGIDTVFGLAFYKAQLAVGNRLPTEGSVFVS 406

Query: 1054 LNDMTKPHLEKIAVSFLELGFKIVATSGTAHFLELKGIPVERVLKLHEGRPHAADMVANG 1113
            + D  KP    +   FLELGF+++ATSGT  +++ KG+ V+ VLK+ EGRPH  DM+ NG
Sbjct: 407  VADKDKPKAVDLVKGFLELGFEVLATSGTYQYMKEKGLEVKHVLKVSEGRPHVVDMIKNG 466

Query: 1114 QIHLMLITSSGDALDQKDGRQLRQMALAYKVPVITTVAGALATAEGIKSLKSSAIKMT-- 1171
            QI L++ T +G    + D   +R+  + Y VP  TTV G  A  E I+  K+S  K+T  
Sbjct: 467  QISLVINTPTGKRA-RTDAYYIRRAVVQYSVPYTTTVRGGYAMLEAIRCYKNSGGKLTVR 525

Query: 1172 ALQDFF 1177
            ALQD F
Sbjct: 526  ALQDIF 531



 Score =  252 bits (643), Expect = 6e-71
 Identities = 150/400 (37%), Positives = 232/400 (58%), Gaps = 19/400 (4%)

Query: 98  LKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETANRTYI 157
           +KK++ILG+GP  IGQ  EFDY+  QA  +LREEG + I+IN NP T+ TD +TA+R Y 
Sbjct: 1   MKKVVILGSGPNRIGQGIEFDYACVQAIFSLREEGVQTIMINCNPETVSTDYDTADRLYF 60

Query: 158 APMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGAIKKA 217
            P+  E V +VI +E+PD +L   GGQT L L++ L ++      GV ++G    +I  A
Sbjct: 61  EPVVLENVLEVIRREKPDGVLIQFGGQTPLKLSLPLRDA------GVTILGTPPESIDIA 114

Query: 218 EDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGIAYNK 277
           EDRELF+  ++ +GL+ PPS    + +E   +AE IG +P+++RP++ LGG    I Y++
Sbjct: 115 EDRELFRRLIQKLGLRQPPSEAVRSKEEAIRVAEAIG-YPVLVRPSYVLGGRAMRIIYDR 173

Query: 278 EEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMGVHTG 337
           EE  +  +  +  S    +L++  L    E +++ + D  ++ ++   +E+I+  GVH+G
Sbjct: 174 EELVTYLEEAVEVSYQRPILIDAYLSDSVEVDVDAIGD-GEDFLVGAVMEHIEEAGVHSG 232

Query: 338 DSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMNPRVS 397
           DS    P  TL     + ++  S  I R +GV  G  N+QFAV   DGEV ++E+NPR S
Sbjct: 233 DSAASIPPYTLPSDVVEEIKRQSKEIARSLGV-VGLINLQFAVK--DGEVYVLEVNPRAS 289

Query: 398 RSSALASKATGFPIAKMAAKLSVGYTL-DQIPNDITRKTPASFEPSIDYV-------VTK 449
           R+    SKA G+P+AK+AAK+S+G  L + +P    R    +  P  D++         K
Sbjct: 290 RTVPFVSKAIGYPLAKLAAKVSIGRKLRELVPEVFRRLEEGNVHPCSDFLPSDWNLYCVK 349

Query: 450 IPRFAFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKA 489
              F + +FP   P+L  +MKS GE M +   F  +F KA
Sbjct: 350 EVVFPWNRFPEVDPVLGPEMKSTGEVMGIDTVFGLAFYKA 389


Lambda     K      H
   0.317    0.133    0.383 

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: 1481
Number of extensions: 75
Number of successful extensions: 12
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1187
Length of database: 532
Length adjustment: 41
Effective length of query: 1146
Effective length of database: 491
Effective search space:   562686
Effective search space used:   562686
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 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis