GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate GFF4005 HP15_3945 aldehyde dehydrogenase family protein

Query= reanno::WCS417:GFF2142
         (499 letters)



>FitnessBrowser__Marino:GFF4005
          Length = 471

 Score =  218 bits (556), Expect = 3e-61
 Identities = 161/481 (33%), Positives = 248/481 (51%), Gaps = 26/481 (5%)

Query: 7   HYINDQRVSRDDRYQDVFNPATGEKTGRVALASRQTVSEAVAAAQAAFAGWADTPPIRRA 66
           +YIN Q VS      DV    TG+   RV  A    + +A+AAA AAF  W+++    R 
Sbjct: 7   NYINGQWVSWAGDMIDVHEAGTGDVIARVPAAGADEMEQAIAAADAAFESWSESTLEERI 66

Query: 67  RVLFEYLHL-LRERKDDLARIIVAEHG---KVFTDAQGEVDRGIDILEFACGIPNLLKGE 122
           +VL E LH  L+ER  ++A  +  E G   K+ T  Q  +   +    +   +P+    E
Sbjct: 67  KVL-EQLHAGLKERAPEIAETVCREVGMPIKLATPIQAGMPAAVT-KSYLKLLPDFPFTE 124

Query: 123 HSDQVSRGMDNWTMRQPLGVVAGVTPFNFPVMVPMWMYPIAIAAGNTFILKPSPTDPSAS 182
            S       ++     P+GVV  +TP+N+P+   +     AIAAG T +LKPS   P  +
Sbjct: 125 QSG------NSEVQYAPVGVVGCITPWNYPLHQVILKIVPAIAAGCTVVLKPSEIAPQTA 178

Query: 183 LFMAELLREAGLPKGVFNVVQGDKESV-DALIEHPDVKAVSFVGSTPIAQYIYETGARNG 241
             +AE+L    LPKGVFN+V G   +V D LI+HPDV+ VSF GST     I    A + 
Sbjct: 179 FILAEILDGTDLPKGVFNMVCGYGHTVGDTLIKHPDVRMVSFTGSTRTGNLIAHAAADDF 238

Query: 242 KRVQGLGGAKNHMVVMPDADIEKTVDALMGAAYGSAGERCMAISVAVLVGDVGDKVIAAL 301
           KR     G K+  V++PDAD+   V   +     ++G+ C A++  ++  D  D+  A  
Sbjct: 239 KRFALEMGGKSASVILPDADLAAAVKGTINNCLLNSGQTCTALTRMLVPADKHDE--ACE 296

Query: 302 TERAKHLRITDGRDLK--AEMGPIVSRAALERISGYIEQGVQAGAQLLLDGRDYVPTEP- 358
              A   ++T G  L+    +GP+ S    +++  YI+ GVQ GA+L+  G    P  P 
Sbjct: 297 LAAAAVAKMTPGNPLEETTRLGPLSSAQQRDKVIDYIKLGVQEGAKLIAGG----PEAPE 352

Query: 359 GLENGFWLGATLFDHVTEEMSIYREEIFGPVLACVRVNDFAEAIKLVNAHEFGNGVSCFT 418
           G E G+++ AT+F +V  +  I +EEIFGPVL  +  ND AEA+K+ N  ++G   + ++
Sbjct: 353 GCEKGYFVKATVFGNVKPDSRIAQEEIFGPVLCVIPYNDEAEAVKIANGTQYGLSGAVWS 412

Query: 419 RDGNIAREFARRIEVGMVGINVPISVPMAWHGFGGWKKSLFGDMHAYGTEGVRFYTKQKS 478
            D   A++ A ++  G V +N     PMA   FGG+  S  G    +G  G+  + + +S
Sbjct: 413 GDDAKAKKIASKLRTGQVFVNGGAFNPMA--PFGGFGHSGIG--REFGKWGLEEFLEVRS 468

Query: 479 I 479
           +
Sbjct: 469 L 469


Lambda     K      H
   0.320    0.136    0.407 

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: 545
Number of extensions: 21
Number of successful extensions: 5
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: 499
Length of database: 471
Length adjustment: 34
Effective length of query: 465
Effective length of database: 437
Effective search space:   203205
Effective search space used:   203205
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 (21.8 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 (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:

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. 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:

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:

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