Alignments for a candidate for asd in Methanococcus maripaludis C5

GapMind for Amino acid biosynthesis

Alignments for a candidate for asd in Methanococcus maripaludis C5

Align Aspartate-semialdehyde dehydrogenase; ASA dehydrogenase; ASADH; Aspartate-beta-semialdehyde dehydrogenase; EC 1.2.1.11 (characterized)
to candidate WP_011867962.1 MMARC5_RS00960 aspartate-semialdehyde dehydrogenase

Query= SwissProt::Q57658
         (354 letters)



>NCBI__GCF_000016125.1:WP_011867962.1
          Length = 348

 Score =  515 bits (1326), Expect = e-151
 Identities = 251/348 (72%), Positives = 294/348 (84%)

Query: 7   MKIKVGVLGATGSVGQRFVQLLADHPMFELTALAASERSAGKKYKDACYWFQDRDIPENI 66
           MKIKVG+LGATG+VGQRF+Q+L +HP+FEL AL AS+RSAGK Y+DACYW+Q   IPE +
Sbjct: 1   MKIKVGILGATGNVGQRFIQMLENHPVFELEALGASQRSAGKTYEDACYWYQTEAIPEEV 60

Query: 67  KDMVVIPTDPKHEEFEDVDIVFSALPSDLAKKFEPEFAKEGKLIFSNASAYRMEEDVPLV 126
               V+ TDP  + ++D+DIVFSALP+DLAK  EPEFAK GK +FSNASA RME DVPL+
Sbjct: 61  ASATVVSTDPNDKAYDDIDIVFSALPADLAKTLEPEFAKRGKYVFSNASAMRMEADVPLI 120

Query: 127 IPEVNADHLELIEIQREKRGWDGAIITNPNCSTICAVITLKPIMDKFGLEAVFIATMQAV 186
           IPEVN +H  ++E+Q+  R  DGAIITNPNCSTI AVI+LKPIMDKFG++ V I TMQA+
Sbjct: 121 IPEVNHEHFGMLEVQKSNRCSDGAIITNPNCSTIGAVISLKPIMDKFGIDLVNITTMQAI 180

Query: 187 SGAGYNGVPSMAILDNLIPFIKNEEEKMQTESLKLLGTLKDGKVELANFKISASCNRVAV 246
           SGAGY+GVPSMAILDNL+P+I  EEEKMQTE+LK+LG+++    +  NFKI  SCNRV V
Sbjct: 181 SGAGYSGVPSMAILDNLVPYIGGEEEKMQTEALKILGSIEGNDFKNGNFKIGVSCNRVPV 240

Query: 247 IDGHTESIFVKTKEGAEPEEIKEVMDKFDPLKDLNLPTYAKPIVIREEIDRPQPRLDRNE 306
           IDGHTESIFVKT E A PEEI +VMD FDPLK LNL +YAKPIV+REE DRPQPRLDRN 
Sbjct: 241 IDGHTESIFVKTTEEATPEEIAKVMDDFDPLKGLNLSSYAKPIVLREENDRPQPRLDRNT 300

Query: 307 GNGMSIVVGRIRKDPIFDVKYTALEHNTIRGAAGASVLNAEYFVKKYI 354
           GNGMSIVVGR+RKDPIF+VKYTALEHNTIRGAAGASVLNAE FV+KY+
Sbjct: 301 GNGMSIVVGRVRKDPIFNVKYTALEHNTIRGAAGASVLNAELFVQKYL 348


Lambda     K      H
   0.317    0.136    0.388 

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: 451
Number of extensions: 12
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: 354
Length of database: 348
Length adjustment: 29
Effective length of query: 325
Effective length of database: 319
Effective search space:   103675
Effective search space used:   103675
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_011867962.1 MMARC5_RS00960 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR00978 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

# 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/TIGR00978.hmm
# target sequence database:        /tmp/gapView.24687.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00978  [M=342]
Accession:   TIGR00978
Description: asd_EA: aspartate-semialdehyde dehydrogenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-138  447.3   0.0     2e-138  447.1   0.0    1.0  1  lcl|NCBI__GCF_000016125.1:WP_011867962.1  MMARC5_RS00960 aspartate-semiald


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000016125.1:WP_011867962.1  MMARC5_RS00960 aspartate-semialdehyde dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  447.1   0.0    2e-138    2e-138       1     341 [.       3     344 ..       3     345 .. 0.98

  Alignments for each domain:
  == domain 1  score: 447.1 bits;  conditional E-value: 2e-138
                                 TIGR00978   1 vkvavLGatGlvGqklvkllekhpyfelakvvaserkaGkkygevvkwilsgdipeevrdleiketepa 69 
                                               +kv++LGatG vGq+++++le+hp fel+++ as+r+aGk+y++++ w+ +  ipeev   ++++t+p+
  lcl|NCBI__GCF_000016125.1:WP_011867962.1   3 IKVGILGATGNVGQRFIQMLENHPVFELEALGASQRSAGKTYEDACYWYQTEAIPEEVASATVVSTDPN 71 
                                               79******************************************************************9 PP

                                 TIGR00978  70 ae.ekdvdlvfsalpsevaeevEkklaeeGlevfsnasalRldpdvplivpEvnsdhlellkvqker.g 136
                                                +  +d+d+vfsalp+++a+ +E+++a++G+ vfsnasa+R++ dvpli+pEvn +h+ +l+vqk    
  lcl|NCBI__GCF_000016125.1:WP_011867962.1  72 DKaYDDIDIVFSALPADLAKTLEPEFAKRGKYVFSNASAMRMEADVPLIIPEVNHEHFGMLEVQKSNrC 140
                                               76689************************************************************8769 PP

                                 TIGR00978 137 wkGvivtnpnCstailtlalkPlidaasikkvivatlqavsGAGypGvssldildnviPyikgEEekie 205
                                                +G i+tnpnCst++  ++lkP++d+++i+ v ++t+qa+sGAGy+Gv+s++ildn++Pyi+gEEek++
  lcl|NCBI__GCF_000016125.1:WP_011867962.1 141 SDGAIITNPNCSTIGAVISLKPIMDKFGIDLVNITTMQAISGAGYSGVPSMAILDNLVPYIGGEEEKMQ 209
                                               9******************************************************************** PP

                                 TIGR00978 206 kEtkkilGkleegkvepaelevsatttRvPvleGHtesvfveldkkldieeirealkefkklpqklglp 274
                                               +E++kilG++e++  ++ ++++ ++++RvPv +GHtes+fv++ ++  +eei + +++f+ l + l+l 
  lcl|NCBI__GCF_000016125.1:WP_011867962.1 210 TEALKILGSIEGNDFKNGNFKIGVSCNRVPVIDGHTESIFVKTTEEATPEEIAKVMDDFDPL-KGLNLS 277
                                               *************************************************************9.99**** PP

                                 TIGR00978 275 saPekpivlldeedrPqprldldaekgmavtvGrlreese.slklvvlghnlvRGAAGaallnaElly 341
                                               s+  kpivl++e+drPqprld+++++gm+++vGr+r++   ++k+  l hn++RGAAGa++lnaEl++
  lcl|NCBI__GCF_000016125.1:WP_011867962.1 278 SY-AKPIVLREENDRPQPRLDRNTGNGMSIVVGRVRKDPIfNVKYTALEHNTIRGAAGASVLNAELFV 344
                                               *9.9*************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (342 nodes)
Target sequences:                          1  (348 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.82
//
[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