Alignments for a candidate for aspA in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for aspA in Klebsiella michiganensis M5al

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate BWI76_RS02330 BWI76_RS02330 aspartate ammonia-lyase

Query= BRENDA::P0AC38
         (478 letters)



>FitnessBrowser__Koxy:BWI76_RS02330
          Length = 478

 Score =  875 bits (2260), Expect = 0.0
 Identities = 437/478 (91%), Positives = 457/478 (95%)

Query: 1   MSNNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAM 60
           M NNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAA 
Sbjct: 1   MLNNIRIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAQ 60

Query: 61  ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLE 120
           ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDV+QGGAGTSVNMNTNEVLANIGLE
Sbjct: 61  ANKELQTIPKSVANAIIAACDEVLNNGKCMDQFPVDVFQGGAGTSVNMNTNEVLANIGLE 120

Query: 121 LMGHQKGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKAVE 180
           LMGHQKGEYQ+LNPNDHVNKCQSTNDAYPTGFRIAVY+S++KL+DAINQL EGF++KAVE
Sbjct: 121 LMGHQKGEYQHLNPNDHVNKCQSTNDAYPTGFRIAVYASILKLIDAINQLSEGFQQKAVE 180

Query: 181 FQDILKMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLN 240
           FQDILKMGRTQLQDAVPMTLGQEF AF++LL EE K I RTAELLLEVNLGATAIGT LN
Sbjct: 181 FQDILKMGRTQLQDAVPMTLGQEFHAFNVLLNEETKCILRTAELLLEVNLGATAIGTRLN 240

Query: 241 TPKEYSPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRL 300
           TP  Y  LAV+KLAEV+  P VPAEDLIEATSDCGAYVMVH +LKRLAVK+SKICNDLRL
Sbjct: 241 TPDGYQQLAVQKLAEVSNLPVVPAEDLIEATSDCGAYVMVHSSLKRLAVKLSKICNDLRL 300

Query: 301 LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQ 360
           LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMA+EAGQLQ
Sbjct: 301 LSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMASEAGQLQ 360

Query: 361 LNVMEPVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPFIG 420
           LNVMEPVIGQAMFES+HILTNACYNLLEKC++GITANK VCE YVYNSIGIVTYLNP+IG
Sbjct: 361 LNVMEPVIGQAMFESIHILTNACYNLLEKCVSGITANKAVCESYVYNSIGIVTYLNPYIG 420

Query: 421 HHNGDIVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTDESEQ 478
           HHNGDIVGKICAETGKSVR+VVLERGLLT AELDDIFS QNLMHPAYKAKRYTDESEQ
Sbjct: 421 HHNGDIVGKICAETGKSVRDVVLERGLLTAAELDDIFSAQNLMHPAYKAKRYTDESEQ 478


Lambda     K      H
   0.317    0.134    0.381 

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: 782
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: 478
Length of database: 478
Length adjustment: 34
Effective length of query: 444
Effective length of database: 444
Effective search space:   197136
Effective search space used:   197136
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 BWI76_RS02330 BWI76_RS02330 (aspartate ammonia-lyase)
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))

# 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.carbon/TIGR00839.hmm
# target sequence database:        /tmp/gapView.15852.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00839  [M=468]
Accession:   TIGR00839
Description: aspA: aspartate ammonia-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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   2.4e-267  873.2   6.3   2.8e-267  873.0   6.3    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS02330  BWI76_RS02330 aspartate ammonia-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS02330  BWI76_RS02330 aspartate ammonia-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  873.0   6.3  2.8e-267  2.8e-267       1     468 []       6     474 ..       6     474 .. 1.00

  Alignments for each domain:
  == domain 1  score: 873.0 bits;  conditional E-value: 2.8e-267
                               TIGR00839   1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakai 71 
                                             rie+dllG++ev+a++yyG++tlra+enf+isn+kisd+pefv+++v+vkkaaa an+el++i++++a+ai
  lcl|FitnessBrowser__Koxy:BWI76_RS02330   6 RIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAQANKELQTIPKSVANAI 76 
                                             89********************************************************************* PP

                               TIGR00839  72 vaacdeile.GkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstnda 141
                                             +aacde+l+ Gk++dqf+vdv+qGGaGtsvnmntnev+an++lel+Gh+kGeyq+lnpndhvnk+qstnda
  lcl|FitnessBrowser__Koxy:BWI76_RS02330  77 IAACDEVLNnGKCMDQFPVDVFQGGAGTSVNMNTNEVLANIGLELMGHQKGEYQHLNPNDHVNKCQSTNDA 147
                                             ********99************************************************************* PP

                               TIGR00839 142 yptalkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkri 212
                                             ypt+++iavy s+ kl+d+i++l ++f+qka+ef+d+lkmGrtqlqdavp+tlGqef+a+ +ll+++ k i
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 148 YPTGFRIAVYASILKLIDAINQLSEGFQQKAVEFQDILKMGRTQLQDAVPMTLGQEFHAFNVLLNEETKCI 218
                                             *********************************************************************** PP

                               TIGR00839 213 krtrelllevnlGataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriav 283
                                              rt+elllevnlGataiGt ln++++y++l+v+klaev+ lp+vpae+lieatsd+gayv+v+++lkr+av
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 219 LRTAELLLEVNLGATAIGTRLNTPDGYQQLAVQKLAEVSNLPVVPAEDLIEATSDCGAYVMVHSSLKRLAV 289
                                             *********************************************************************** PP

                               TIGR00839 284 klskvcndlrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlq 354
                                             klsk+cndlrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvt+a+eaGqlq
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 290 KLSKICNDLRLLSSGPRAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMASEAGQLQ 360
                                             *********************************************************************** PP

                               TIGR00839 355 lnvlepviafallesisiltnaiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakea 425
                                             lnv+epvi++a++esi+iltna+++l++kcv Gitan+ +ce+yv+nsiGivt+lnp+iG++++++v+k++
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 361 LNVMEPVIGQAMFESIHILTNACYNLLEKCVSGITANKAVCESYVYNSIGIVTYLNPYIGHHNGDIVGKIC 431
                                             *********************************************************************** PP

                               TIGR00839 426 iktgksvrdvvlekdllteeelddilsvenllkpaykakklkd 468
                                             ++tgksvrdvvle++llt +elddi+s++nl++paykak+++d
  lcl|FitnessBrowser__Koxy:BWI76_RS02330 432 AETGKSVRDVVLERGLLTAAELDDIFSAQNLMHPAYKAKRYTD 474
                                             ****************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (468 nodes)
Target sequences:                          1  (478 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: 00:00:00.02
# Mc/sec: 9.05
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources