Alignments for a candidate for argH in Sinorhizobium meliloti 1021

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Sinorhizobium meliloti 1021

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate SMc00725 SMc00725 argininosuccinate lyase

Query= BRENDA::Q8DVX5
         (460 letters)



>FitnessBrowser__Smeli:SMc00725
          Length = 467

 Score =  454 bits (1169), Expect = e-132
 Identities = 231/454 (50%), Positives = 306/454 (67%), Gaps = 1/454 (0%)

Query: 2   TTKNHKLWGGRFEAGLAQWVEEFGASISFDQKLAEFDLKGSIAHVTMLGEKGIISQEDAA 61
           T  ++++WGGRF +G    +EE  ASI FD+KL   D++GSIAH TML  +GIIS ED  
Sbjct: 8   TKSSNQMWGGRFASGPDAIMEEINASIGFDKKLYAQDIRGSIAHATMLAHQGIISAEDKD 67

Query: 62  TIKAGLEDLLEEYKAGQLKFDVSNEDIHMNMESLLTAKIGPVAGKLHTARSRNDQVATDM 121
            I  GL+ +L E  +G  +F    EDIHMN+E+ L A IGP AG+LHTARSRNDQVA D 
Sbjct: 68  KIVHGLDTILSEIDSGAFEFSRRLEDIHMNIEARLAALIGPAAGRLHTARSRNDQVALDF 127

Query: 122 HLYLKAKLDEVIEKLANLRTVLVDLADKHVHTIMPGYTHLQHAQPISFGHHLMAYYNMFT 181
            L++K +L +  + L  L    +D A++H  T+MPG+THLQ AQP++FGHH MAY  MF 
Sbjct: 128 RLWVKEELQKTEKALTGLIAAFLDRAEEHAETVMPGFTHLQTAQPVTFGHHCMAYVEMFG 187

Query: 182 RDSERFIFNVKHTDLSPLGAAALAGTTFPIDREMTAQLMGFAEPYSNSLDAVSDRDFILE 241
           RD  R    ++H D SP+GAAALAGT FPIDR MTA+ +GF EP  NS+D VSDRDF LE
Sbjct: 188 RDRARVRHAIEHMDESPIGAAALAGTGFPIDRHMTAKALGFREPTRNSIDTVSDRDFALE 247

Query: 242 FLSNASILMMHMSRMCEEVISWCSHEYQFVTLSDTFSTGSSIMPQKKNPDMAELIRGKSG 301
           FLS A+I   H+SR+ EE++ W + ++ F+ LSD FSTGSSIMPQKKNPD AEL+R K+G
Sbjct: 248 FLSIAAIAATHLSRLAEEIVIWSTPQFGFIRLSDAFSTGSSIMPQKKNPDAAELVRAKTG 307

Query: 302 RVYANLFGLLTVMKALPLAYNKDLQEDKEGMFDTAETITVALDILAGMLSSMIVNDKHMA 361
           RV  +L  LLTVMK LPLAY+KD+QEDKE +FD AE++ +A+  + GM+  + +    M 
Sbjct: 308 RVNGSLVALLTVMKGLPLAYSKDMQEDKEQVFDAAESLELAIAAMTGMIRDVTIRADRMK 367

Query: 362 ESTQKDFSNATELADYLASK-GMPFRQAHEIVGKLILECSKNGHYLQDVPLERYQTISDL 420
            +    +S AT+LAD+L  + G+PFR AH + G+++    + G  L D+PL   Q I+  
Sbjct: 368 AAAGSGYSTATDLADWLVREAGLPFRDAHHVTGRVVALAEQKGCDLADLPLAELQAINSA 427

Query: 421 IEEDVYETLKSHTAVERRHSLGGTGFEQVKWQIA 454
           I + VY  L    +V  R S GGT   +V+ QIA
Sbjct: 428 ITDKVYGVLTVEASVASRTSFGGTAPSEVRKQIA 461


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: 596
Number of extensions: 29
Number of successful extensions: 2
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: 467
Length adjustment: 33
Effective length of query: 427
Effective length of database: 434
Effective search space:   185318
Effective search space used:   185318
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 SMc00725 SMc00725 (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.18230.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.8e-189  615.0   0.1   5.4e-189  614.8   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc00725  SMc00725 argininosuccinate lyase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc00725  SMc00725 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  614.8   0.1  5.4e-189  5.4e-189       1     452 [.      14     465 ..      14     467 .] 0.99

  Alignments for each domain:
  == domain 1  score: 614.8 bits;  conditional E-value: 5.4e-189
                           TIGR00838   1 lwggRlkkeldkavaefnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkegklele 75 
                                         +wggR+++++d  ++e nas+ fDk+l+++Di+gsiah+++La++gi+++e+++k++++L+++ +e+++g++e++
  lcl|FitnessBrowser__Smeli:SMc00725  14 MWGGRFASGPDAIMEEINASIGFDKKLYAQDIRGSIAHATMLAHQGIISAEDKDKIVHGLDTILSEIDSGAFEFS 88 
                                         6************************************************************************** PP

                           TIGR00838  76 vdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalvekAekevetlmp 150
                                            eDiH+++E++l + +g  ++++lht+rsRnDqva d+rl++++++++  +al  l++a++++Ae++ et+mp
  lcl|FitnessBrowser__Smeli:SMc00725  89 RRLEDIHMNIEARLAALIG-PAAGRLHTARSRNDQVALDFRLWVKEELQKTEKALTGLIAAFLDRAEEHAETVMP 162
                                         *******************.7778*************************************************** PP

                           TIGR00838 151 gytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidrellaelLgFdavvensld 225
                                         g+tHLq AqP+t++Hh++ay+em+ rD  R+  a++ +++sP+G++Alagt+f+idr+++a+ LgF + ++ns+d
  lcl|FitnessBrowser__Smeli:SMc00725 163 GFTHLQTAQPVTFGHHCMAYVEMFGRDRARVRHAIEHMDESPIGAAALAGTGFPIDRHMTAKALGFREPTRNSID 237
                                         *************************************************************************** PP

                           TIGR00838 226 avsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssimPqKKnpDvaEliRgktgrviGn 300
                                         +vsdRDf++E+ls aa++++hlsrlaEe++++s+  fgf+ lsd++s+gssimPqKKnpD+aEl+R+ktgrv+G+
  lcl|FitnessBrowser__Smeli:SMc00725 238 TVSDRDFALEFLSIAAIAATHLSRLAEEIVIWSTPQFGFIRLSDAFSTGSSIMPQKKNPDAAELVRAKTGRVNGS 312
                                         *************************************************************************** PP

                           TIGR00838 301 ltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllkelkvnkerleeaakknfalatdlAdylvrk 375
                                         l++llt++K+lPlaY kD+qEdke++fda + +e ++ ++tg++++++++ +r++ aa +++++atdlAd+lvr+
  lcl|FitnessBrowser__Smeli:SMc00725 313 LVALLTVMKGLPLAYSKDMQEDKEQVFDAAESLELAIAAMTGMIRDVTIRADRMKAAAGSGYSTATDLADWLVRE 387
                                         *************************************************************************** PP

                           TIGR00838 376 .GvPFReaheivGevvakaiekGkkleeltleelqklsekleedvlevldleeavekrdakGGtakeevekaiee 449
                                          G+PFR+ah+++G+vva a++kG +l +l+l+elq+++++++++v+ vl++e +v+ r++ GGta++ev+k+i+ 
  lcl|FitnessBrowser__Smeli:SMc00725 388 aGLPFRDAHHVTGRVVALAEQKGCDLADLPLAELQAINSAITDKVYGVLTVEASVASRTSFGGTAPSEVRKQIAW 462
                                         *************************************************************************97 PP

                           TIGR00838 450 aka 452
                                          +a
  lcl|FitnessBrowser__Smeli:SMc00725 463 WRA 465
                                         765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (467 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: 8.46
//
[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