GapMind for catabolism of small carbon sources

 

Aligments for a candidate for puuC in Herbaspirillum seropedicae SmR1

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate HSERO_RS04810 HSERO_RS04810 aldehyde dehydrogenase

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS04810 HSERO_RS04810 aldehyde
           dehydrogenase
          Length = 504

 Score =  324 bits (830), Expect = 5e-93
 Identities = 191/478 (39%), Positives = 264/478 (55%), Gaps = 14/478 (2%)

Query: 22  AFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGV---WSQL 78
           ++INGE   A  GE  +  +P  GR     AS    D   A   A A         W  L
Sbjct: 25  SWINGELV-AGQGEIIQLYNPATGR-----ASLSYRDGGAAAVEAAAVAAQRAQRQWWAL 78

Query: 79  APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138
           + A R   L     ++R   E LA LE +  GKPI D  + ++   A+   + A   DK 
Sbjct: 79  SHAARGRALYAVGAVIRAEAEPLARLEAISSGKPIRDCRA-EMQKVAEMFEYYAGWADKF 137

Query: 139 YDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198
           Y EV P P   L    REP G V  + PWN P     W+LGPALATGN+V+LKPSE +P 
Sbjct: 138 YGEVIPVPSSHLNYTRREPYGTVLQMTPWNAPAFTCGWQLGPALATGNAVLLKPSELTPF 197

Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258
           +++ IA+L  +AG+PAG++NVL G G T+         V  ++F GS      L+  A  
Sbjct: 198 SSLAIARLGEQAGLPAGLVNVLAGLGQTMVPQAMATWTVKKVIFVGSPATGA-LIAKAAA 256

Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318
           + +    LE GGKS NI+F DA DL+ AA  A +AI    G+ C AGSRLLV+R + D+F
Sbjct: 257 ARVMPCVLELGGKSANIIFEDA-DLRLAAFGAQAAIFSGAGQSCVAGSRLLVQRKVYDRF 315

Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378
           +  V    +  + G PLD  T VG + + +Q   +   +  G + GA L AG  R  EE 
Sbjct: 316 VETVAAGAEKIRLGAPLDDSTEVGPINNRKQYEHIQRMVARGLEAGATLAAGHTRYGEE- 374

Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438
            G +V PT+    +NAM +A+ EIFGPV   I F+  EEA+AIAND+ +GLA  +WT D+
Sbjct: 375 -GYFVRPTLLAHASNAMEVARSEIFGPVAVAIPFEDEEEAIAIANDSEFGLAGAVWTRDV 433

Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496
           ++AH+ A +V AG+ WVN Y   ++ +PFGGF +SG GR   + AL  YT+ K+ W++
Sbjct: 434 ARAHRVAASVNAGTFWVNSYKTINVASPFGGFNRSGYGRSSGMEALYDYTQTKSVWVE 491


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: 618
Number of extensions: 26
Number of successful extensions: 4
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: 497
Length of database: 504
Length adjustment: 34
Effective length of query: 463
Effective length of database: 470
Effective search space:   217610
Effective search space used:   217610
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: 52 (24.6 bits)

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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, or view the source code.

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