Alignments for a candidate for argH in Methylosarcina fibrata AML-C10

GapMind for Amino acid biosynthesis

Alignments for a candidate for argH in Methylosarcina fibrata AML-C10

Align Argininosuccinate lyase; ASAL; EC 4.3.2.1; Arginosuccinase (uncharacterized)
to candidate WP_020562013.1 A3OW_RS23915 argininosuccinate lyase

Query= curated2:Q12X66
         (491 letters)



>NCBI__GCF_000372865.1:WP_020562013.1
          Length = 509

 Score =  217 bits (552), Expect = 9e-61
 Identities = 145/457 (31%), Positives = 233/457 (50%), Gaps = 8/457 (1%)

Query: 9   RLASVPDEEIIN--FTSSMNADKWIFKADILVDLAHTIMLKERKIIKAEDCKKILEGLLT 66
           RL S P   ++   F   ++    +F+A    DLA+T+   E   I  E  +++L  LL 
Sbjct: 20  RLKSAPAANMVQSVFALELSHQNGLFEAMGQADLAYTLTAMELNTIPLEAGRQLLASLLE 79

Query: 67  IKEEGIE-KLDHTYEDIHISLESRLIDMVGEDTGGRMHSGRSRNDEVATCIRLTLRNDLL 125
           ++ + +    D    D++ + E+ L +    D  G + +GR+R +       + +R +LL
Sbjct: 80  LQAKPVSFDTDPARGDMYTNREAWLAERT--DAVGWLGAGRARREATTAAFFIVMREELL 137

Query: 126 LLMEELIALRNTLNDTSSENLNTLMPGFTHLQHAQPTTLAHHLTAHANAIGRDLERTMDC 185
            L + ++ L   L   +  +  ++MP +T+LQ AQPTT  H+L   A  + RDLER    
Sbjct: 138 ELGQAVVRLAEALVAQADAHKQSVMPDYTYLQAAQPTTFGHYLLGFAYPLLRDLERLEAL 197

Query: 186 YKRVNLSPLGAAAFASTGFDLDRERTCKLLGFDGLIENSMDAVSSRDFLIESASVFANLM 245
           + R N SP+G  +   +     R +  +LLGF G+IE+  DA+   D  IE+AS+     
Sbjct: 198 FARFNRSPMGCGSTNGSRLAQGRRQMAELLGFAGVIEHGRDAMWQPDLCIETASILTACA 257

Query: 246 INLSKVAEEIVIWSTSEFAFIELDDRYASTSSIMPQKKNPDTAELLRGKSGVTIGSLMSL 305
           INLS++AE++ I+ T EF  +ELDD +A  S IMPQKKNP     +RG +   IG   S+
Sbjct: 258 INLSRLAEDLQIYGTQEFGLVELDDSHARASKIMPQKKNPFALTHIRGVANRMIGLSASV 317

Query: 306 LAICKALPLSYNRDLQEATPNIMQSLETTRASVRIMNGMIATMSINKENMAGLATAGFTT 365
            A  +  P     +       + +++     +V +M  ++A +S N E    L  +G+  
Sbjct: 318 SATART-PSGQPDNRLFLYGELPEAMTLVLNAVELMAEVLAKISFNSERGRQLVASGWVM 376

Query: 366 ATELADTMVRVCDIPFRTAHQIVGVLARGSGEPTLGEIDAVAHNVIGESLSSRGL--TEK 423
           AT+LA+T+V+ C + FR AH++V  LA    E  L E+D    N  GE +  R L  TE 
Sbjct: 377 ATDLAETLVQECGLDFRGAHRLVASLASEFPEKNLRELDHDTVNRFGEIILGRRLAVTEN 436

Query: 424 MVKEALDPILNVSKRSVIGGPSPESMERLIESSRERI 460
            +  ALD    +  R   GG +   M+R++   RER+
Sbjct: 437 QLSMALDAHRALEARKEPGGTAVACMDRMMAECRERL 473


Lambda     K      H
   0.317    0.132    0.366 

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: 469
Number of extensions: 23
Number of successful extensions: 4
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: 491
Length of database: 509
Length adjustment: 34
Effective length of query: 457
Effective length of database: 475
Effective search space:   217075
Effective search space used:   217075
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: 52 (24.6 bits)

Align candidate WP_020562013.1 A3OW_RS23915 (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.25007.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.3e-87  280.6   0.0    1.7e-87  280.3   0.0    1.0  1  lcl|NCBI__GCF_000372865.1:WP_020562013.1  A3OW_RS23915 argininosuccinate l


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000372865.1:WP_020562013.1  A3OW_RS23915 argininosuccinate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.3   0.0   1.7e-87   1.7e-87       4     454 ..      19     473 ..      17     474 .. 0.91

  Alignments for each domain:
  == domain 1  score: 280.3 bits;  conditional E-value: 1.7e-87
                                 TIGR00838   4 gRlkkeldkavae..fnaslsfDkelaeaDiegsiahtkaLakagilteeeakklieaLeelkeevkeg 70 
                                               +Rlk+++  ++ +  f+  ls+ + l+ea  ++++a+t + ++ + +  e  ++l ++L el+ +  + 
  lcl|NCBI__GCF_000372865.1:WP_020562013.1  19 SRLKSAPAANMVQsvFALELSHQNGLFEAMGQADLAYTLTAMELNTIPLEAGRQLLASLLELQAKPVS- 86 
                                               567766655553323888899999**************************************998877. PP

                                 TIGR00838  71 klelevdaeDiHlavErelidkvgedvgkklhtgrsRnDqvatdlrlylrdkvkelaealkdllkalve 139
                                                +++++   D++++ E+ l +++   vg  l +gr+R +  ++ + + +r+++ el +a+  l +alv 
  lcl|NCBI__GCF_000372865.1:WP_020562013.1  87 -FDTDPARGDMYTNREAWLAERTD-AVG-WLGAGRARREATTAAFFIVMREELLELGQAVVRLAEALVA 152
                                               .9********************98.666.**************************************** PP

                                 TIGR00838 140 kAekevetlmpgytHLqrAqPitlaHhllayaemlerDleRlldalkRvnksPlGsgAlagtsfeidre 208
                                               +A+++++ +mp yt+Lq AqP+t++H+ll +a  l rDleRl   + R n+sP+G+g   g+ ++  r+
  lcl|NCBI__GCF_000372865.1:WP_020562013.1 153 QADAHKQSVMPDYTYLQAAQPTTFGHYLLGFAYPLLRDLERLEALFARFNRSPMGCGSTNGSRLAQGRR 221
                                               ********************************************************************* PP

                                 TIGR00838 209 llaelLgFdavvensldavsdRDfiiEllsaaallmvhlsrlaEelilfsseEfgfvelsdevssgssi 277
                                               ++aelLgF+ v+e+  da+ + D  iE+ s ++ ++++lsrlaE+l ++ ++Efg+vel+d+ + +s i
  lcl|NCBI__GCF_000372865.1:WP_020562013.1 222 QMAELLGFAGVIEHGRDAMWQPDLCIETASILTACAINLSRLAEDLQIYGTQEFGLVELDDSHARASKI 290
                                               ********************************************************************* PP

                                 TIGR00838 278 mPqKKnpDvaEliRgktgrviGnltglltilKalPlaYnkDlqEdkealfdalktveellevvtgllke 346
                                               mPqKKnp ++  iRg + r+iG  +++ ++ + +P+    +      +l +a++ v +++e+++ +l++
  lcl|NCBI__GCF_000372865.1:WP_020562013.1 291 MPQKKNPFALTHIRGVANRMIGLSASVSATAR-TPSGQPDNRLFLYGELPEAMTLVLNAVELMAEVLAK 358
                                               **********************7666666655.56655444445677899******************* PP

                                 TIGR00838 347 lkvnkerleeaakknfalatdlAdylvrk.GvPFReaheivGevvakaiekGk.kleeltleelqkl.. 411
                                               + +n+er +++++++++ atdlA++lv++ G+ FR ah++v +++ +  ek + +l++ t++++ ++  
  lcl|NCBI__GCF_000372865.1:WP_020562013.1 359 ISFNSERGRQLVASGWVMATDLAETLVQEcGLDFRGAHRLVASLASEFPEKNLrELDHDTVNRFGEIil 427
                                               **********************************************99999555666666666655533 PP

                                 TIGR00838 412 ..sekleed.vlevldleeavekrdakGGtakeevekaieeakael 454
                                                 + +++e+ +  +ld ++a+e+r+  GGta + + ++++e +++l
  lcl|NCBI__GCF_000372865.1:WP_020562013.1 428 grRLAVTENqLSMALDAHRALEARKEPGGTAVACMDRMMAECRERL 473
                                               3334566666*******************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (455 nodes)
Target sequences:                          1  (509 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: 9.45
//
[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