GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Herbaspirillum seropedicae SmR1

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>FitnessBrowser__HerbieS:HSERO_RS17580
          Length = 440

 Score =  197 bits (500), Expect = 7e-55
 Identities = 137/415 (33%), Positives = 204/415 (49%), Gaps = 49/415 (11%)

Query: 26  VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGK--FWHTGNGYTNEPV 83
           V GEG  L DQ GK YID +GG AV+ LGH HPR+++A+ +Q G+  + HT + +T  P 
Sbjct: 17  VAGEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELAYAHT-SFFTTAPA 75

Query: 84  LRLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGR 141
             LA  L DA     + V+F + G+EA EAALKLAR+Y  +    ++  I+A + ++HG 
Sbjct: 76  EELAAMLADAAPGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRRHIIARRQSYHGN 135

Query: 142 TLFTVSAGGQPAYSQDFAPLPPQIQHAI-----------YNDLDSAKALID--------- 181
           TL  ++ GG     + F P+  +  H              +D+   + L D         
Sbjct: 136 TLGALAIGGNAWRREMFMPMLIEAHHVSPCYAYRNRADGESDVQYVQRLADELEQKILSL 195

Query: 182 --DNTCAVIVEPMQGE-GGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAY 238
             D   A + E + G   G VP   D+ R +R +CD +  LLI DEV +G+GRTG L+A 
Sbjct: 196 GADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVMSGMGRTGYLFAC 255

Query: 239 MHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVGT----HGTTYGGNPLACAVAG 293
              GV PD++  AK LG G+ PIGA++ S+     +  G+    HG TY G+  ACA A 
Sbjct: 256 EEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGSGFFQHGHTYIGHATACAAAV 315

Query: 294 EVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKA-- 351
            V  TI    +L  V+QR +     L           +IRG GL +G  L  E + K   
Sbjct: 316 AVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGVELVAERSSKLPL 375

Query: 352 -------KAISNQAAEEGLMILIAGANV-------VRFAPALIISEDEVNSGLDR 392
                    +  +A + GL++   G  +       +  AP  I S ++++  + R
Sbjct: 376 SPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSNDISEIVQR 430


Lambda     K      H
   0.321    0.137    0.412 

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: 434
Number of extensions: 28
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: 406
Length of database: 440
Length adjustment: 32
Effective length of query: 374
Effective length of database: 408
Effective search space:   152592
Effective search space used:   152592
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: 50 (23.9 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