GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00870 in Herbaspirillum seropedicae SmR1

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate HSERO_RS17350 HSERO_RS17350 ABC transporter substrate-binding protein

Query= uniprot:A0A165KTD4
         (375 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS17350 HSERO_RS17350 ABC
           transporter substrate-binding protein
          Length = 380

 Score =  415 bits (1067), Expect = e-121
 Identities = 216/377 (57%), Positives = 264/377 (70%), Gaps = 5/377 (1%)

Query: 3   LKLKLTVV---AAIAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNA 59
           +KLK  ++   AAI  A   A+  ++VVKI HV P+SG  AH GKDNENGARMA++ELNA
Sbjct: 1   MKLKSAIIPLTAAIGLAFAGAAYSQEVVKIAHVGPLSGPNAHMGKDNENGARMAVDELNA 60

Query: 60  QGVTIGGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDC 119
           +G TIGGKK+KFELV EDDA+DPKQ TA A KL D KVA V+GHLNSGTTIPASK+Y+D 
Sbjct: 61  KGFTIGGKKVKFELVGEDDASDPKQATAVATKLVDQKVAAVIGHLNSGTTIPASKIYSDA 120

Query: 120 GIPHVTGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQ 179
           GIP V+ +ATNP  T+ G+KT FR++AND  LGA L  YAV  L  K +A+IDDRTAYGQ
Sbjct: 121 GIPQVSPSATNPKYTQQGFKTAFRVVANDAQLGAALGKYAVQKLGTKQIAVIDDRTAYGQ 180

Query: 180 GVADVFKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQ 239
           GVAD F K A A G  +V  Q+T DKATDF AILT++K K PD +F+GGMD  GGPMLRQ
Sbjct: 181 GVADEFAKGAKAAGGTIVGTQYTNDKATDFNAILTSLKGKKPDVVFFGGMDAVGGPMLRQ 240

Query: 240 MEQLGMGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAE-GGSSLAKMPGGTAWKAKYDA 298
           M+QLG+ + K+ GGDGICT  +  LA        VICAE GG   A   G   ++A Y  
Sbjct: 241 MKQLGI-SAKFMGGDGICTGSLPGLAGDGLGDDQVICAEAGGVDEAGKKGMDDFRAAYKK 299

Query: 299 KYPNQFQVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMK 358
           K+       + Y YDAT  + DAM +A S DPK Y PELAK S KGVT  IAF+  G++K
Sbjct: 300 KFGIDVVYNAAYAYDATMTVADAMAKAGSADPKKYLPELAKISHKGVTGVIAFDAKGDIK 359

Query: 359 NPAITLYVYKDGKKTPL 375
           + ++TLY YK G++T L
Sbjct: 360 DGSLTLYTYKGGQRTLL 376


Lambda     K      H
   0.315    0.131    0.375 

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: 539
Number of extensions: 17
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: 375
Length of database: 380
Length adjustment: 30
Effective length of query: 345
Effective length of database: 350
Effective search space:   120750
Effective search space used:   120750
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: 42 (22.0 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 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