GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2396 in Acidovorax sp. GW101-3H11

Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Ac3H11_552 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)

Query= uniprot:A0A165KTD4
         (375 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_552
          Length = 384

 Score =  513 bits (1322), Expect = e-150
 Identities = 247/371 (66%), Positives = 294/371 (79%), Gaps = 1/371 (0%)

Query: 6   KLTVVAAIAAAAGVASAQE-QVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTI 64
           +++ + A+A AA VASAQ+ Q VKI H  PVSG  AH GKD ENG R+AI++LNAQ + I
Sbjct: 13  RISALTAVALAASVASAQDVQTVKIAHAGPVSGGIAHIGKDTENGVRLAIDDLNAQNLVI 72

Query: 65  GGKKIKFELVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHV 124
           GGKKIKFE+ AEDDA DP+Q TA AQKLCD KVAGVVGHL SGT+IPAS +Y  C +PH+
Sbjct: 73  GGKKIKFEIAAEDDAGDPRQATAVAQKLCDQKVAGVVGHLQSGTSIPASAIYAKCDLPHI 132

Query: 125 TGAATNPNLTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADV 184
           T +A+NP+LTKPG+KTTFR+IANDNALGA LA +  D  KLK+VAIIDDRTAYGQGVA V
Sbjct: 133 TASASNPDLTKPGHKTTFRLIANDNALGAALALFGADHQKLKSVAIIDDRTAYGQGVASV 192

Query: 185 FKKTATAKGMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLG 244
           FK TA  KG+KVV E+FT DKATDFMAILTAIK K PDAIFYGG+D Q GPMLRQMEQLG
Sbjct: 193 FKATAQQKGLKVVAEEFTNDKATDFMAILTAIKNKKPDAIFYGGLDAQAGPMLRQMEQLG 252

Query: 245 MGNVKYFGGDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQF 304
           +GNVKYFGGD +CT ++ +L+     L NV CA GG+S+ KM GG  WK +YDAK+P QF
Sbjct: 253 LGNVKYFGGDALCTEKLPELSGKTPALKNVTCATGGASVDKMQGGADWKKRYDAKFPGQF 312

Query: 305 QVYSPYTYDATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITL 364
           Q+YSPY YDA  ++ DAMKRANSVDPKV+ P LAK+ +KGVT+ IAF   GE+  PA+TL
Sbjct: 313 QIYSPYAYDAAMVLADAMKRANSVDPKVFAPFLAKTEYKGVTANIAFTAKGELTTPAVTL 372

Query: 365 YVYKDGKKTPL 375
           Y +KDG +  L
Sbjct: 373 YTFKDGSRVAL 383


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: 511
Number of extensions: 15
Number of successful extensions: 1
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: 384
Length adjustment: 30
Effective length of query: 345
Effective length of database: 354
Effective search space:   122130
Effective search space used:   122130
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 (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