Alignments for a candidate for argH in Chlorobaculum tepidum TLS

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Chlorobaculum tepidum TLS

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate NP_661946.1 CT1055 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>NCBI__GCF_000006985.1:NP_661946.1
          Length = 463

 Score =  436 bits (1120), Expect = e-126
 Identities = 218/452 (48%), Positives = 310/452 (68%)

Query: 8   LWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAATIKAGL 67
           LW  RF     +   +F +S+  D  L   D++GSIAH TMLGE+GIIS+E+A  I  GL
Sbjct: 11  LWQSRFSEPFDREALKFSSSVHVDGLLYREDIQGSIAHATMLGEQGIISKEEAGQIVTGL 70

Query: 68  EDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDMHLYLKA 127
           + + +E ++G+L     +EDIH  +E+ L   IGP AGKLH+ RSRNDQVATD  LYL+ 
Sbjct: 71  KAVEKEIESGELTPVWEDEDIHTVIENRLKELIGPTAGKLHSGRSRNDQVATDTRLYLRR 130

Query: 128 KLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFTRDSERF 187
            +D + E L  +++ L+D A+++ HTIM GYTHLQ AQPIS GH+ MA+++MF RD++R 
Sbjct: 131 NIDRIGELLKAMQSTLLDKAEQYKHTIMFGYTHLQRAQPISAGHYYMAWHSMFGRDAQRL 190

Query: 188 IFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILEFLSNAS 247
               K  ++SPLGAAA AG+T P+D   +A+L+ F   ++NS+DAVSDRD ++EF+S  S
Sbjct: 191 ADLRKRANISPLGAAAFAGSTLPLDPARSAELLEFDGVFTNSIDAVSDRDLVIEFVSACS 250

Query: 248 ILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSGRVYANL 307
           ++MMH+SR  E+VI W S E+ ++++SD F+TGSSIMPQKKN D+AEL+RGK+GRVY NL
Sbjct: 251 MIMMHLSRFSEDVILWSSAEFNYLSISDAFATGSSIMPQKKNADIAELVRGKTGRVYGNL 310

Query: 308 FGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMAESTQKD 367
             LLT+MK LPL+YN+D+QEDK  +FDTAET   +L +   M+    +N++ +A  T +D
Sbjct: 311 MNLLTIMKGLPLSYNRDMQEDKPPLFDTAETTASSLSVFRRMIEKTWLNEERLARLTAED 370

Query: 368 FSNATELADYLASKGMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDLIEEDVYE 427
            S ATE+A+YL  K +PFR AH I GK++    + G  L  + L+ Y+T S+  +E +Y+
Sbjct: 371 LSLATEIAEYLVKKQIPFRDAHRITGKIVAYAIEQGKTLPTISLDEYRTFSEAFDEGIYD 430

Query: 428 TLKSHTAVERRHSLGGTGFEQVKWQIAEAKKA 459
            LK   +V  + + G   F+ V+ QIA AK A
Sbjct: 431 DLKPDASVNSKKTAGSCSFKSVEEQIARAKAA 462


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: 587
Number of extensions: 21
Number of successful extensions: 1
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: 463
Length adjustment: 33
Effective length of query: 427
Effective length of database: 430
Effective search space:   183610
Effective search space used:   183610
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 NP_661946.1 CT1055 (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.31687.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                              -----------
   6.6e-183  594.8   0.0   7.4e-183  594.6   0.0    1.0  1  lcl|NCBI__GCF_000006985.1:NP_661946.1  CT1055 argininosuccinate lyase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000006985.1:NP_661946.1  CT1055 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  594.6   0.0  7.4e-183  7.4e-183       1     452 [.      11     461 ..      11     463 .] 0.99

  Alignments for each domain:
  == domain 1  score: 594.6 bits;  conditional E-value: 7.4e-183
                              TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegkl 72 
                                            lw++R+++  d ++ +f++s++ D  l+++Di+gsiah+++L ++gi+++eea +++ +L+ +++e+++g+l
  lcl|NCBI__GCF_000006985.1:NP_661946.1  11 LWQSRFSEPFDREALKFSSSVHVDGLLYREDIQGSIAHATMLGEQGIISKEEAGQIVTGLKAVEKEIESGEL 82 
                                            7*********************************************************************** PP

                              TIGR00838  73 elevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAeke 144
                                            ++ +++eDiH+++E++l + +g   ++klh+grsRnDqvatd rlylr +++++ e lk+++++l++kAe+ 
  lcl|NCBI__GCF_000006985.1:NP_661946.1  83 TPVWEDEDIHTVIENRLKELIG-PTAGKLHSGRSRNDQVATDTRLYLRRNIDRIGELLKAMQSTLLDKAEQY 153
                                            **********************.6666********************************************* PP

                              TIGR00838 145 vetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgF 216
                                            ++t+m gytHLqrAqPi+ +H+ +a+++m+ rD +Rl d  kR+n sPlG++A+ag+++++d+ ++aelL F
  lcl|NCBI__GCF_000006985.1:NP_661946.1 154 KHTIMFGYTHLQRAQPISAGHYYMAWHSMFGRDAQRLADLRKRANISPLGAAAFAGSTLPLDPARSAELLEF 225
                                            ************************************************************************ PP

                              TIGR00838 217 davvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaE 288
                                            d v +ns+davsdRD +iE++sa++++m+hlsr++E++il+ss+Ef+++++sd++++gssimPqKKn+D+aE
  lcl|NCBI__GCF_000006985.1:NP_661946.1 226 DGVFTNSIDAVSDRDLVIEFVSACSMIMMHLSRFSEDVILWSSAEFNYLSISDAFATGSSIMPQKKNADIAE 297
                                            ************************************************************************ PP

                              TIGR00838 289 liRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakk 360
                                            l+Rgktgrv+Gnl+ llti+K+lPl+Yn+D+qEdk++lfd+ +t+ ++l+v++ ++++  +n+erl++++++
  lcl|NCBI__GCF_000006985.1:NP_661946.1 298 LVRGKTGRVYGNLMNLLTIMKGLPLSYNRDMQEDKPPLFDTAETTASSLSVFRRMIEKTWLNEERLARLTAE 369
                                            ************************************************************************ PP

                              TIGR00838 361 nfalatdlAdylvrkGvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekr 432
                                            + +lat++A+ylv+k +PFR+ah+i+G++va+aie+Gk+l  ++l+e++ +se+++e +++ l++  +v+ +
  lcl|NCBI__GCF_000006985.1:NP_661946.1 370 DLSLATEIAEYLVKKQIPFRDAHRITGKIVAYAIEQGKTLPTISLDEYRTFSEAFDEGIYDDLKPDASVNSK 441
                                            ************************************************************************ PP

                              TIGR00838 433 dakGGtakeevekaieeaka 452
                                            +++G  ++++ve++i+ aka
  lcl|NCBI__GCF_000006985.1:NP_661946.1 442 KTAGSCSFKSVEEQIARAKA 461
                                            *****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (463 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: 7.32
//
[ok]

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