Alignments for a candidate for putA in Hippea alviniae EP5-r

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Hippea alviniae EP5-r

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_022671215.1 G415_RS0108295 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::P30038
         (563 letters)



>NCBI__GCF_000420385.1:WP_022671215.1
          Length = 544

 Score =  509 bits (1311), Expect = e-148
 Identities = 251/530 (47%), Positives = 359/530 (67%), Gaps = 2/530 (0%)

Query: 34  NEPVLAFTQGSPERDALQKALKDLKGRMEAIPCVVGDEEVWTSDVQYQVSPFNHGHKVAK 93
           NEPV ++  G+ ER+ L++A+K++K +   IP ++G EE+ T +V   V P +    +  
Sbjct: 13  NEPVYSYAPGTEEREKLKEAIKEIKSQEIEIPLIIGGEEIKTGNVAKIVEPHDTKSVLGV 72

Query: 94  FCYADKSLLNKAIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQGK 153
           +  A +  +N AI+AA+ A K+W      DRA IFLKAA++LS   R  I A TM+   K
Sbjct: 73  YHMAGEKEINMAIDAAMQAAKKWREYDWIDRAAIFLKAAELLSTKYRYLINAATMLSLSK 132

Query: 154 TVIQAEIDAAAELIDFFRFNAKYAVELEGQQPISVPPST-NSTVYRGLEGFVAAISPFNF 212
            V QAEID+A ELIDF RFN  Y  ++  +QP+  P  T N   YR LEGF+ A+ PFNF
Sbjct: 133 NVFQAEIDSACELIDFLRFNLFYMQKIYEEQPLYSPKGTWNIMQYRPLEGFIFAVPPFNF 192

Query: 213 TAIGGNLAGAPALMGNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272
            +I GNL  APA+MGNVVLWKP+++++ A Y   +IL+EAGLP  +I F+PA G   G  
Sbjct: 193 VSIAGNLPTAPAMMGNVVLWKPAESSVYAPYIFMKILQEAGLPDGVINFIPAIGREIGHF 252

Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332
           V +SEH  GI+FTGSVPTF  +W+ +A+N+ ++  +PR+ GE GGK++ FVH+SA+   +
Sbjct: 253 VFASEHFAGIHFTGSVPTFNKMWQMMAENIHKYKAYPRIVGETGGKDYIFVHKSANRRKL 312

Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVI 392
           ++  +R A+EY GQKCSA SR+Y+P S+W +IK  L +E  +IK+G P EDF  F +A+I
Sbjct: 313 ITAIVRGAYEYQGQKCSAVSRVYIPKSMWSEIKDDLFKEIDKIKMGSP-EDFTNFMNALI 371

Query: 393 DAKSFARIKKWLEHARSSPSLTILAGGKCDDSVGYFVEPCIVESKDPQEPIMKEEIFGPV 452
           D K+F ++  ++++A+++    I+ GG  D+S G+FVEP ++ +++P    M+EEIFGPV
Sbjct: 372 DEKAFKKVTSYIDYAKNASDAEIVKGGGYDNSKGWFVEPTVILTENPHFKTMEEEIFGPV 431

Query: 453 LSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRNAAGNFYINDKSTG 512
           +++Y Y DDKY ETL L D T+ YGLTGA+FS+D+D  + A  +L  +AGNFYINDK TG
Sbjct: 432 VTIYPYDDDKYIETLHLCDQTSPYGLTGAIFSEDRDATRVAIDILEGSAGNFYINDKPTG 491

Query: 513 SIVGQQPFGGARASGTNDKPGGPHYILRWTSPQVIKETHKPLGDWSYAYM 562
           ++VGQQPFGG R SGTNDK G    +LRW +P+ IKE       + Y +M
Sbjct: 492 AVVGQQPFGGTRGSGTNDKAGSHLNLLRWVTPRAIKENFIAPESFEYPFM 541


Lambda     K      H
   0.319    0.135    0.411 

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: 853
Number of extensions: 41
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: 563
Length of database: 544
Length adjustment: 36
Effective length of query: 527
Effective length of database: 508
Effective search space:   267716
Effective search space used:   267716
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_022671215.1 G415_RS0108295 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01236 (pruA: 1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.132208.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 1-pyrroline-5-carboxylate 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.9e-242  790.9   0.2   3.3e-242  790.7   0.2    1.0  1  NCBI__GCF_000420385.1:WP_022671215.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000420385.1:WP_022671215.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  790.7   0.2  3.3e-242  3.3e-242       2     532 ..      13     541 ..      12     542 .. 0.99

  Alignments for each domain:
  == domain 1  score: 790.7 bits;  conditional E-value: 3.3e-242
                             TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                           nePv +++pg++er++l++++ke+ks+ +eiPl+igg+e+ + +++ ++v+P+d +++l++ + a+e++++ a
  NCBI__GCF_000420385.1:WP_022671215.1  13 NEPVYSYAPGTEEREKLKEAIKEIKSQEIEIPLIIGGEEIKT-GNVAKIVEPHDTKSVLGVYHMAGEKEINMA 84 
                                           9**************************************655.557*************************** PP

                             TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147
                                           ++aa++a k+W e ++ draaiflkaa+lls+kyr+ i+aatml+ sk+v+qaeid+++elidf+rfn+ y +
  NCBI__GCF_000420385.1:WP_022671215.1  85 IDAAMQAAKKWREYDWIDRAAIFLKAAELLSTKYRYLINAATMLSLSKNVFQAEIDSACELIDFLRFNLFYMQ 157
                                           ************************************************************************* PP

                             TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220
                                           +++e qP  s +g++n ++yrpleGf++a++Pfnf++ia+nl++aPa+mGnvv+WkP++ +v++ y+ mkil+
  NCBI__GCF_000420385.1:WP_022671215.1 158 KIYEEQPLYSPKGTWNIMQYRPLEGFIFAVPPFNFVSIAGNLPTAPAMMGNVVLWKPAESSVYAPYIFMKILQ 230
                                           ********9**************************************************************** PP

                             TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293
                                           eaGlP gvinf+pa g +++  v a++++a++hftGs+++f+++w+++a+n++ky+ +PrivGetGGkd+++v
  NCBI__GCF_000420385.1:WP_022671215.1 231 EAGLPDGVINFIPAIGREIGHFVFASEHFAGIHFTGSVPTFNKMWQMMAENIHKYKAYPRIVGETGGKDYIFV 303
                                           ************************************************************************* PP

                             TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksf 366
                                           h+sa+ +++++a++rga+eyqGqkcsa+sr+y+pks+w e+k++l++e +k+k+g ++d+++fm a+idek+f
  NCBI__GCF_000420385.1:WP_022671215.1 304 HKSANRRKLITAIVRGAYEYQGQKCSAVSRVYIPKSMWSEIKDDLFKEIDKIKMGSPEDFTNFMNALIDEKAF 376
                                           ************************************************************************* PP

                             TIGR01236 367 akivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilev 439
                                           +k+ ++i++ak+ + + ei+ GG yd+skG+fvePtv+++++P+ k+m+eeifGPv+t+y ydddky e+l++
  NCBI__GCF_000420385.1:WP_022671215.1 377 KKVTSYIDYAKNAS-DAEIVKGGGYDNSKGWFVEPTVILTENPHFKTMEEEIFGPVVTIYPYDDDKYIETLHL 448
                                           ***********955.9********************************************************* PP

                             TIGR01236 440 vdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfv 512
                                            d+ts y+ltGa+f++dr+a + a + l  +aGnfyindk+tGavvgqqpfGG+r sGtndkaG+  +llr+v
  NCBI__GCF_000420385.1:WP_022671215.1 449 CDQTSPYGLTGAIFSEDRDATRVAIDILEGSAGNFYINDKPTGAVVGQQPFGGTRGSGTNDKAGSHLNLLRWV 521
                                           ************************************************************************* PP

                             TIGR01236 513 sarsiketfkeltdfkypym 532
                                           ++r+ike+f +++ f+yp+m
  NCBI__GCF_000420385.1:WP_022671215.1 522 TPRAIKENFIAPESFEYPFM 541
                                           ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (544 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 11.26
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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