Alignments for a candidate for argH in Caulobacter crescentus NA1000

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Caulobacter crescentus NA1000

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate CCNA_02294 CCNA_02294 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>FitnessBrowser__Caulo:CCNA_02294
          Length = 472

 Score =  399 bits (1025), Expect = e-115
 Identities = 213/454 (46%), Positives = 287/454 (63%), Gaps = 1/454 (0%)

Query: 8   LWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAGL 67
           +WGGRF A  A+ ++    SI FD++L   DL GS AH  ML  +G+I+  D   I  GL
Sbjct: 18  MWGGRFSAKPAELMQAINVSIGFDKRLWAQDLAGSRAHARMLMNQGVIASHDGEEILEGL 77

Query: 68  EDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLKA 127
             + +E  +G   F    EDIHMN+E+ L   IGP AG+LHTARSRNDQVA D  L+++ 
Sbjct: 78  ARVEDELLSGTFPFRDEYEDIHMNIEARLRELIGPTAGRLHTARSRNDQVAVDFRLWVRD 137

Query: 128 KLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDSERF 187
             D  + +L  L+  L+  A+ H  ++MPG+THLQ AQP++FGHHLMAY  MF RD+ RF
Sbjct: 138 ACDRTVGQLEALQKALLTQAEAHAESLMPGFTHLQPAQPVTFGHHLMAYVEMFGRDAGRF 197

Query: 188 IFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNAS 247
                  +  PLGAAALAG+ FPIDR+ TA  +GF  P +NSLD+VS RDF LE LS AS
Sbjct: 198 RDARARMNECPLGAAALAGSPFPIDRQQTASALGFDRPTANSLDSVSSRDFALEALSAAS 257

Query: 248 ILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYANL 307
           I   H+SR+ EE++ W +  + F+ L+D F+TGSSIMPQKKNPD AELIR K GR+  +L
Sbjct: 258 ITATHLSRLAEEIVLWTTPMFGFIKLTDAFTTGSSIMPQKKNPDAAELIRAKVGRILGSL 317

Query: 308 FGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAESTQKD 367
             L  VMK LPLAY+KD+QEDK   F+  + + ++L  +AGM++ +  N ++MA++    
Sbjct: 318 TTLTVVMKGLPLAYSKDMQEDKVPTFEAFDALELSLLAMAGMIADLTPNTENMAKAAGAG 377

Query: 368 FSNATELADYLA-SKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDVY 426
           FS AT+LAD+L  +  MPFR AH + G  +      G  L D+ L ++Q I   I ++VY
Sbjct: 378 FSTATDLADWLVRTLNMPFRDAHHVTGSAVKTAEGLGVDLADLSLAQFQAIEPQITKEVY 437

Query: 427 ETLKSHTAVERRHSLGGTGFEQVKWQIAEAKKAL 460
             L    +   R S GGT   QV+ QIA  K+ L
Sbjct: 438 AVLTPAASAASRMSYGGTAPAQVRAQIARWKELL 471


Lambda     K      H
   0.318    0.132    0.378 

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: 529
Number of extensions: 17
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: 460
Length of database: 472
Length adjustment: 33
Effective length of query: 427
Effective length of database: 439
Effective search space:   187453
Effective search space used:   187453
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: 51 (24.3 bits)

Align candidate CCNA_02294 CCNA_02294 (argininosuccinate lyase)
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

# 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.aa/TIGR00838.hmm
# target sequence database:        /tmp/gapView.9034.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00838  [M=455]
Accession:   TIGR00838
Description: argH: argininosuccinate lyase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-178  580.7   0.0   1.4e-178  580.5   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02294  CCNA_02294 argininosuccinate lya


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02294  CCNA_02294 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  580.5   0.0  1.4e-178  1.4e-178       1     453 [.      18     470 ..      18     472 .] 0.99

  Alignments for each domain:
  == domain 1  score: 580.5 bits;  conditional E-value: 1.4e-178
                             TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkle 73 
                                           +wggR++ ++ + +++ n s+ fDk+l ++D+ gs ah+++L+++g++ + + +++ e+L+++++e  +g++ 
  lcl|FitnessBrowser__Caulo:CCNA_02294  18 MWGGRFSAKPAELMQAINVSIGFDKRLWAQDLAGSRAHARMLMNQGVIASHDGEEILEGLARVEDELLSGTFP 90 
                                           6************************************************************************ PP

                             TIGR00838  74 levdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekeve 146
                                           +++++eDiH+++E++l + +g   +++lht+rsRnDqva+d+rl++rd+ ++ + +l++l+kal+ +Ae++ e
  lcl|FitnessBrowser__Caulo:CCNA_02294  91 FRDEYEDIHMNIEARLRELIG-PTAGRLHTARSRNDQVAVDFRLWVRDACDRTVGQLEALQKALLTQAEAHAE 162
                                           *********************.6666*********************************************** PP

                             TIGR00838 147 tlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdav 219
                                            lmpg+tHLq AqP+t++Hhl+ay+em+ rD  R+ da  R+n++PlG++Alag+ f+idr+++a+ LgFd+ 
  lcl|FitnessBrowser__Caulo:CCNA_02294 163 SLMPGFTHLQPAQPVTFGHHLMAYVEMFGRDAGRFRDARARMNECPLGAAALAGSPFPIDRQQTASALGFDRP 235
                                           ************************************************************************* PP

                             TIGR00838 220 vensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRg 292
                                           ++nsld+vs+RDf++E+lsaa+++++hlsrlaEe++l+++  fgf++l+d++++gssimPqKKnpD+aEliR+
  lcl|FitnessBrowser__Caulo:CCNA_02294 236 TANSLDSVSSRDFALEALSAASITATHLSRLAEEIVLWTTPMFGFIKLTDAFTTGSSIMPQKKNPDAAELIRA 308
                                           ************************************************************************* PP

                             TIGR00838 293 ktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfala 365
                                           k gr+ G+lt+l +++K+lPlaY kD+qEdk + f+a + +e +l +++g++++l+ n+e++++aa ++f++a
  lcl|FitnessBrowser__Caulo:CCNA_02294 309 KVGRILGSLTTLTVVMKGLPLAYSKDMQEDKVPTFEAFDALELSLLAMAGMIADLTPNTENMAKAAGAGFSTA 381
                                           ************************************************************************* PP

                             TIGR00838 366 tdlAdylvrk.GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGG 437
                                           tdlAd+lvr   +PFR+ah+++G++v++a+  G++l +l+l+++q+++++++++v+ vl++  + + r+++GG
  lcl|FitnessBrowser__Caulo:CCNA_02294 382 TDLADWLVRTlNMPFRDAHHVTGSAVKTAEGLGVDLADLSLAQFQAIEPQITKEVYAVLTPAASAASRMSYGG 454
                                           ************************************************************************* PP

                             TIGR00838 438 takeevekaieeakae 453
                                           ta+++v+ +i+  k+ 
  lcl|FitnessBrowser__Caulo:CCNA_02294 455 TAPAQVRAQIARWKEL 470
                                           ***********99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (472 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.70
//
[ok]

This GapMind analysis is from Apr 09 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