Alignments for a candidate for puuC in Verminephrobacter eiseniae EF01-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for puuC in Verminephrobacter eiseniae EF01-2

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011810430.1 VEIS_RS13090 aldehyde dehydrogenase family protein

Query= metacyc::MONOMER-11560
         (497 letters)



>NCBI__GCF_000015565.1:WP_011810430.1
          Length = 798

 Score =  327 bits (838), Expect = 1e-93
 Identities = 198/468 (42%), Positives = 272/468 (58%), Gaps = 19/468 (4%)

Query: 21  RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80
           R FI+GE+      E FE  +P     LA+VA    AD ++AV  AR    +  WS L+ 
Sbjct: 35  RHFIHGEFVAPAQNEYFEVFNPATEERLARVAHGSDADIDQAVAAARQALPA--WSGLSG 92

Query: 81  AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140
            +R   L   A  L+K+    A+LET+D GK I +S  IDIP   +  +  A    ++ D
Sbjct: 93  HQRARYLYAIARHLQKHARFFAVLETMDNGKTIRESRDIDIPLVVRHFYHHA-GWAQLLD 151

Query: 141 EVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200
              P           + VGV G IVPWNFPLLM  WK+ PALA GN+VVLKP+E +PLTA
Sbjct: 152 SEFPA---------HQAVGVCGQIVPWNFPLLMLAWKVAPALAAGNTVVLKPAEFTPLTA 202

Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESN 260
           +  A+L +E G+PAGVLN++ G GHT G +L  H  VD + FTGST + + L+  A    
Sbjct: 203 LAFAELCVEVGLPAGVLNIVTGDGHT-GASLVNHAGVDKIAFTGSTAVGR-LIRRATAGT 260

Query: 261 MKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLP 320
            K++ LE GGKSP IVF DA DL AA E    +I FNQG+VC AGSR+LV+ S+  +F  
Sbjct: 261 DKKLSLELGGKSPFIVFDDA-DLDAAVEGVVDSIWFNQGQVCCAGSRILVQESVAARFGD 319

Query: 321 MVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLE-ETG 379
            +   ++  + GNPLD    VGA+VD  Q+  +   +E+G  DG   L+  +  L+  + 
Sbjct: 320 KLRARMRKLRIGNPLDKSNDVGAIVDRVQLQRIRQMVESGRADG---LSCWQTALDAPSS 376

Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439
           G +  PT F+ V  A  +AQEEIFGPV+  + F T +EAVA+AN + YGLAA +W+ +I 
Sbjct: 377 GHFFAPTFFEDVPAAHALAQEEIFGPVVISMGFRTLDEAVALANHSRYGLAASLWSENID 436

Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKY 487
                A  + AG VWVN  +  D  A FGG+++SG GR+     + +Y
Sbjct: 437 VCLTVAAQLAAGVVWVNGANMFDAAAGFGGYRESGFGREGGREGMHEY 484



 Score = 90.5 bits (223), Expect = 2e-22
 Identities = 81/256 (31%), Positives = 115/256 (44%), Gaps = 8/256 (3%)

Query: 13  AQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNS 72
           A+ +    + +I G+     SG +F   S   G  L      +  D   AVE AR    +
Sbjct: 517 ARSIDRSAKFYIGGKQVRPDSGYSFGVRSG-SGALLGHAGFGNRKDIRNAVETAR---KA 572

Query: 73  GVWSQLAPAKRKAKLIRFADLLRKNVEE-LALLETLDMGKPIGDSSSIDIPGAAQAIHWT 131
           G WSQ +   R   L  FA+ L    +  +A L+ +D       S   +    A+  H+ 
Sbjct: 573 GNWSQASGHARAQVLYYFAENLGARAQTFIAHLQAIDGISEAAASQQFE-QVLARVFHYA 631

Query: 132 AEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLK 191
           A A DK    V  T    + L   EP GVVG   P + PLL A     P LATGN VVL 
Sbjct: 632 AMA-DKHDGSVHSTLTAHVTLAMNEPFGVVGVRSPAHTPLLAALSLALPLLATGNRVVLV 690

Query: 192 PSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQ 251
           P   + L    + Q+   + +PAGVLN++ G    + + LALH DVD L + G    A +
Sbjct: 691 PPPDASLMFADLYQVLDTSDMPAGVLNIVWGDSDELAEVLALHDDVDALWYFGPAAGAAR 750

Query: 252 LMVYAGESNMKRIWLE 267
           +   A   N+K  W++
Sbjct: 751 VQA-ASAGNLKSTWVQ 765


Lambda     K      H
   0.316    0.132    0.390 

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: 1049
Number of extensions: 60
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 497
Length of database: 798
Length adjustment: 38
Effective length of query: 459
Effective length of database: 760
Effective search space:   348840
Effective search space used:   348840
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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