Alignments for a candidate for icd in Magnetospirillum magneticum AMB-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for icd in Magnetospirillum magneticum AMB-1

Align isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) (characterized)
to candidate WP_011383051.1 AMB_RS03140 isocitrate dehydrogenase (NADP(+))

Query= BRENDA::B7GQR3
         (406 letters)



>NCBI__GCF_000009985.1:WP_011383051.1
          Length = 406

 Score =  602 bits (1553), Expect = e-177
 Identities = 292/404 (72%), Positives = 342/404 (84%), Gaps = 2/404 (0%)

Query: 1   MAKIKVEGTVVELDGDEMTRVIWKDIKDRLILPYLDVNLDYYDLGIEHRDETDDQVTIDA 60
           M KIKV   +VELDGDEMTR+IWK IKD+LILPYLDV+L YYDLGIE+RD+TDD+VTI+A
Sbjct: 1   MNKIKVANPIVELDGDEMTRIIWKFIKDKLILPYLDVDLKYYDLGIEYRDKTDDKVTIEA 60

Query: 61  AHAIQKHHVGVKCATITPDEARVKEFGLKKMWKSPNGTIRNILGGTIFREPIVMSNVPRL 120
           + AI+K+ VGVKCATITPDEARVKEF LKKMWKSPNGTIRNIL GT+FREPI+  NVPRL
Sbjct: 61  SEAIKKYGVGVKCATITPDEARVKEFNLKKMWKSPNGTIRNILDGTVFREPIICKNVPRL 120

Query: 121 VPGWTKPIVVARHAFGDQYKATDFKVPGAGQLTVTFTPDDGSEPIQHVVYNYGEDGGVAQ 180
           VPGWTKPIV+ RHAFGDQYKATDF VPG G+LT+ F   +G E I+H V+++    GVA 
Sbjct: 121 VPGWTKPIVIGRHAFGDQYKATDFTVPGPGKLTIKFVGTNG-ETIEHEVFDF-PGAGVAM 178

Query: 181 VQYNVNDSIRGFARACFNYGLMRHYPVYLSTKNTILKAYDGQFKDIFAEVFETEYKDKYA 240
             YN+++SI GFARAC NYG  + +PVYLSTKNTILKAYDG+FKDIF EV+E E+K +YA
Sbjct: 179 GMYNLDESIYGFARACLNYGQQKKWPVYLSTKNTILKAYDGRFKDIFQEVYEKEFKAEYA 238

Query: 241 EAGLTYEHRLIDDMVASSLKWHGGYIWACKNYDGDVQSDSVAQGFGSLGLMTSVLMTPDG 300
           + G+TYEHRLIDDMVAS+LKW G ++WACKNYDGDVQSD+VAQGFGSLGLMTSVLM+PDG
Sbjct: 239 KLGITYEHRLIDDMVASALKWSGEFVWACKNYDGDVQSDTVAQGFGSLGLMTSVLMSPDG 298

Query: 301 QTVESEAAHGTVTRHYRRWQKGEKTSTNPIASIFAWTGGLKHRADLDGTPEVRHFAKTLE 360
           + VE+EAAHGTVTRHYR  QKG++TSTNPIASIFAWT GL +RA  D TPEV  FA+ LE
Sbjct: 299 KVVEAEAAHGTVTRHYREHQKGKETSTNPIASIFAWTRGLFYRAQFDNTPEVAKFAQALE 358

Query: 361 KVIVDTVEGGQMTKDLAMLIGPDEPWLDTDGFMNALDENLAKAL 404
           +V V+TVE G MTKDLA+LIGP + WL T  F++ LDENL K +
Sbjct: 359 EVCVETVESGFMTKDLAILIGPGQSWLTTQQFLDKLDENLKKRM 402


Lambda     K      H
   0.318    0.136    0.416 

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: 681
Number of extensions: 24
Number of successful extensions: 3
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: 406
Length of database: 406
Length adjustment: 31
Effective length of query: 375
Effective length of database: 375
Effective search space:   140625
Effective search space used:   140625
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: 50 (23.9 bits)

Align candidate WP_011383051.1 AMB_RS03140 (isocitrate dehydrogenase (NADP(+)))
to HMM TIGR00127 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

# 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/TIGR00127.hmm
# target sequence database:        /tmp/gapView.16008.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00127  [M=409]
Accession:   TIGR00127
Description: nadp_idh_euk: isocitrate dehydrogenase, NADP-dependent
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.1e-221  719.1   0.2   7.1e-221  718.9   0.2    1.0  1  lcl|NCBI__GCF_000009985.1:WP_011383051.1  AMB_RS03140 isocitrate dehydroge


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009985.1:WP_011383051.1  AMB_RS03140 isocitrate dehydrogenase (NADP(+))
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.9   0.2  7.1e-221  7.1e-221       2     407 ..       3     402 ..       2     404 .. 0.99

  Alignments for each domain:
  == domain 1  score: 718.9 bits;  conditional E-value: 7.1e-221
                                 TIGR00127   2 kikvanpvveldgdemtriiwelikdklilpyleldlkyydlsvesrdatndkvtkdaaeaikkynvav 70 
                                               kikvanp+veldgdemtriiw+ ikdklilpyl++dlkyydl++e+rd+t+dkvt +a+eaikky+v+v
  lcl|NCBI__GCF_000009985.1:WP_011383051.1   3 KIKVANPIVELDGDEMTRIIWKFIKDKLILPYLDVDLKYYDLGIEYRDKTDDKVTIEASEAIKKYGVGV 71 
                                               9******************************************************************** PP

                                 TIGR00127  71 kcatitpdearvkefklkkmwkspngtirnilggtvfrepiiikriprlvprwekpiiigrhafgdqyk 139
                                               kcatitpdearvkef+lkkmwkspngtirnil+gtvfrepii+k++prlvp+w+kpi+igrhafgdqyk
  lcl|NCBI__GCF_000009985.1:WP_011383051.1  72 KCATITPDEARVKEFNLKKMWKSPNGTIRNILDGTVFREPIICKNVPRLVPGWTKPIVIGRHAFGDQYK 140
                                               ********************************************************************* PP

                                 TIGR00127 140 atdvvvpgpgklklvykpkdgaekvdlkvydyeeeggvalamyntdesiedfakaslklalekklplyl 208
                                               atd+ vpgpgkl + ++  + +e+++ +v+d+++ g va++myn desi +fa+a l+   +kk+p+yl
  lcl|NCBI__GCF_000009985.1:WP_011383051.1 141 ATDFTVPGPGKLTIKFVGTN-GETIEHEVFDFPGAG-VAMGMYNLDESIYGFARACLNYGQQKKWPVYL 207
                                               ****************9875.6899*********98.******************************** PP

                                 TIGR00127 209 stkntilkkydgrfkdifqevyekqykskfealgiwyehrliddmvaqalkskggyilalknydgdvqs 277
                                               stkntilk ydgrfkdifqevyek++k  + +lgi yehrliddmva alk  g +++a+knydgdvqs
  lcl|NCBI__GCF_000009985.1:WP_011383051.1 208 STKNTILKAYDGRFKDIFQEVYEKEFKAEYAKLGITYEHRLIDDMVASALKWSGEFVWACKNYDGDVQS 276
                                               ********************************************************************* PP

                                 TIGR00127 278 divaqgfgslglmtsvlvtpdgktveaeaahgtvtrhyrkyqkgeetstnsiasifawsrgllkrakld 346
                                               d+vaqgfgslglmtsvl++pdgk veaeaahgtvtrhyr++qkg+etstn+iasifaw+rgl  ra++d
  lcl|NCBI__GCF_000009985.1:WP_011383051.1 277 DTVAQGFGSLGLMTSVLMSPDGKVVEAEAAHGTVTRHYREHQKGKETSTNPIASIFAWTRGLFYRAQFD 345
                                               ********************************************************************* PP

                                 TIGR00127 347 ntaelvkfaeilesatietveegimtkdlalilkksklersayltteefldaveerlkkkl 407
                                               nt+e++kfa++le++++etve+g+mtkdla++++      +++ltt++fld+++e+lkk++
  lcl|NCBI__GCF_000009985.1:WP_011383051.1 346 NTPEVAKFAQALEEVCVETVESGFMTKDLAILIGPG----QSWLTTQQFLDKLDENLKKRM 402
                                               *********************************998....89****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (409 nodes)
Target sequences:                          1  (406 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.80
//
[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